Bioinformatics Links Directory - Search for Links with keyword 'gene expression'

Gene Expression Data Analyzer

Fri, 18 May 2012 02:00:18 -0400

The Gene Expression Data Analyzer (GEDA) is a tool for discovering differential gene expression in a subset of patients. It is tailored to cancer-related microarray studies and offers extensive options for visualization, classification and normalization.

Gene Expression Database (GXD)

Sun, 20 May 2012 05:40:05 -0400

The Gene Expression Database (GXD) is a community resource of mouse developmental expression information. GXD integrates different types of expression data at the transcript and protein level and captures expression information from many different mouse strains and mutants. GXD places these data in the larger biological context through integration with other Mouse Genome Informatics (MGI) resources and interconnections with many other databases. Web-based query forms support simple or complex searches. All data are annotated and reviewed by GXD curators.

Gene Expression Barcode

Mon, 21 May 2012 02:50:10 -0400

Gene Expression Barcode is a database that provides reliable absolute measures of expression for most annotated genes for human and mouse tissue types, including diseased tissue. This is made possible by an algorithm that leverages information from the GEO and ArrayExpress public repositories to build statistical models that permit converting data from a single microarray into expressed/unexpressed calls for each gene. For selected platforms, users may upload data and obtain results.

Microarray Gene Expression Database

Sun, 03 Oct 2010 00:45:29 -0400

Group facilitating the development of an international repository for gene expression data and the experimental and database standards required for such an endeavour.

Mouse Atlas of Gene Expression

Sun, 03 Oct 2010 00:45:34 -0400

A quantitative and comprehensive atlas of gene expression in mouse development. The project has a goal of producing 150 publically available SAGE libraries.

Pancreatic Expression database

Sun, 20 May 2012 19:10:05 -0400

The Pancreatic Expression database (PED) is a repository for pancreatic-derived -omics data. It includes easurements derived from transcriptomics, proteomics, genomics and miRNA profiles from various pancreas-centred reports on a broad range of specimen and experimental types.

TIGR Gene Indices

Sat, 19 May 2012 20:10:17 -0400

An analysis of a set of unique, highly accurate virtual transcripts that are represented in the worlds public EST data; can perform a BLAST search against the TIGR unique Gene Indices.

Expression Profiler

Fri, 18 May 2012 07:50:07 -0400

Expression Profiler is a web based platform for microarray data analysis developed at the EBI. This resource is integrated with the ArrayExpress database, a public repository for microarray data.

BIOBASE Gene Regulation databases

Sat, 19 May 2012 06:30:06 -0400

includes: TRANSFAC - transcription factor database; Patho DB - mutated forms of transcription factors and binding sites that are pathologically relevant; S/MARt DB - scaffold matrix transaction database; TRANSPATH - gene regulatory pathway database.

Gene Set Builder

Tue, 15 May 2012 12:30:11 -0400

Gene Set Builder is a database-driven, web-based tool designed to help researchers compile, store, export, and share sets of genes. This application supports the 17 eukaryotic genomes found in version 32 of the Ensembl database, which includes species from yeast to human. User-created information such as sets and customized annotations are stored and can be shared to facilitate easy access. Gene sets stored in the system can be exported in a variety of output formats - as lists of identifiers, in tables, or as sequences.

Gene Regulation

Sun, 03 Oct 2010 00:45:14 -0400

Access to databases, programs and papers related to gene regulation.

Mammalian Gene Collection

Sat, 19 May 2012 09:20:05 -0400

Goal is to provide a complete set of full-length (open reading frame) sequences and cDNA clones of expressed genes for human and mouse; publicly accessible.

GeneSigDB

Sun, 20 May 2012 09:30:10 -0400

GeneSigDB is a manually curated database of gene expression signatures. GeneSigDB focuses on cancer, development, and stem cell gene signatures and was constructed from thousands of publications from which we manually transcribe gene signatures. Gene signatures are mapped to the genome to extract standardized lists of EnsEMBL gene identifiers. GeneSigDB provides the original gene signature, the standardized gene list and a fully traceable gene mapping history for each gene from the original transcribed data table through to the standardized list of genes. GeneSigDB release 3.0 (Decemeber 2010) contained over 2,000 gene signatures.

ToppCluster - comparative enriched features network generator and analyzer

Sun, 20 May 2012 07:20:07 -0400

ToppCluster is a human/mammalian genomes-centered web server application for comparative enrichment and network analysis of multiple gene lists. Features such as Gene Ontology terms, protein interactions,disease or disease-associated mammalian phenotypes, promoter cis-elements, miR binding sites, etc. that are differentially represented in the gene lists can be clustered or transformed into high dimensional Cytoscape or Gephi -compatible networks.

GeneCAT

Sat, 19 May 2012 16:40:14 -0400

The Gene Co-expression Analysis Tool-box (GeneCAT) is a suite of microarray co-expression analysis tools for plant biology. The platform includes both standard co-expression tools such as gene clustering and expression profiling, as well as tools that combine co-expression analysis with BLAST for functional inferencing. Arabidopsis thaliana and Barley are featured plants.

GeneSet2miRNA

Mon, 21 May 2012 05:00:07 -0400

GeneSet2miRNA is a web based tool for identification of miRNA regulatory activity within an input gene list. A list of miRNA regulatory models is output.

GeneExpress2.1

Mon, 14 May 2012 22:40:07 -0400

Integrated system for data analysis with information about expression and gene networks, also contains transcriptional regulatory regions database (TRRD).

PubGene

Sat, 19 May 2012 21:40:14 -0400

Searchable literature network of human genes with tools for gene expression analysis. Choose from the free public service, or purchase the commercial package.

SPEED

Sat, 19 May 2012 19:10:09 -0400

Signaling Pathway Enrichment using Experimental Datasets (SPEED) is a web server for enrichment of signaling pathways responsible for gene expression changes.

GeneCodis

Fri, 18 May 2012 02:20:16 -0400

Originally designed in 2007 for modular enrichment analysis, GeneCodis assists in functional analysis of gene lists, integrating information from different sources. GeneCodis also finds regulatory patterns, and singular and modular patterns of interrelated annotations.

Network of Cancer Genes

Sun, 20 May 2012 14:30:05 -0400

The Network of Cancer Genes (NCG) collects and integrates data on 736 human genes that are mutated in various types of cancer. For each gene, NCG provides information on duplicability, orthology, evolutionary appearance and topological properties of the encoded protein in a comprehensive version of the human protein-protein interaction network. NCG also stores information on all primary interactors of cancer proteins, thus providing a complete overview of 5357 proteins that constitute direct and indirect determinants of human cancer.

MAGIA

Sat, 19 May 2012 22:10:08 -0400

miRNA and Genes Integrated Analysis (MAGIA) is a web tool for the integrative analysis of target predictions, miRNA and gene expression data

GeneTrail

Sat, 19 May 2012 16:30:15 -0400

GeneTrail analyzes gene sets for statistically significant accumulations of genes belonging to functional categories. Two common statistical approaches are implemented including: Over-Representation Analysis (ORA) for comparing a reference set of genes to a test set; and, Gene Set Enrichment Analysis (GSEA) for scoring sorted lists of genes.

RiceXPro

Mon, 21 May 2012 04:20:07 -0400

RiceXPro is a gene expression database to provide the transcriptional changes throughout the growth of the rice plant in the field. RiceXPro contains two data sets corresponding to spatiotemporal gene expression profiles of various organs and tissues, and continuous gene expression profiles of leaf from transplanting to harvesting. A user-friendly web interface enables the extraction of specific gene expression profiles by keyword and chromosome search, and basic data analysis, thereby providing useful information as to the organ/tissue and developmental stage specificity of expression of a particular gene. Analysis tools such as t-test, calculation of fold change and degree of correlation facilitate the comparison of expression profiles between two random samples and the prediction of function of uncharacterized genes.

miRvestigator

Sun, 20 May 2012 08:00:12 -0400

miRvestigator is a web based tool to identify miRNAs mediating co-regulation of gene expression patterns observed in transcriptome profilng data. The miRvestigator takes as input a list of co-expressed genes and returns the most likely miRNA regulating the genes. It searches for an over-represented sequence motif in the 3' UTRs of the genes using Weeder and compares the motif to all unique miRNA seed sequences in miRBase using our custom built miRvestigator hidden Markov model (HMM).

FANTOM

Mon, 21 May 2012 04:40:06 -0400

The Functional Annotation Of the Mammalian Genome (FANTOM) is a database for the transcriptional network that regulates macrophage differentiation. Data comes from cap analysis of gene expression (CAGE), sequencing mRNA 5'-ends with a second-generation sequencer to quantify promoter activities even in the absence of gene annotation. Additional genome-wide experiments complement the setup including short RNA sequencing, microarray gene expression profiling on large-scale perturbation experiments and ChIP-chip for epigenetic marks and transcription factors.

Targetfinder.org

Thu, 17 May 2012 16:00:04 -0400

Targetfinder.org provides a web based resource that allows users to find genes that have a similar expression to a query gene signature.

GenePublisher

Sat, 19 May 2012 15:50:03 -0400

GenePublisher performs automatic normalization, statistical analysis, and visualization of DNA microarray data.

Babelomics

Sat, 19 May 2012 13:30:13 -0400

Babelomics is a suite of web tools for the functional annotation and analysis of groups of genes in high throughput experiments. Tools include: FatiGO, FatiGOplus, Fatiscan, Gene Set Enrichment Analysis (GSEA), Marmite, and the Tissues Mining Tool (TMT). Other tools include Biocarta pathways, Transfac and a tool de novo functional annotation of sequences.

GeneHub-GEPIS

Sun, 13 May 2012 16:00:14 -0400

GeneHub-GEPIS is a tool for inferring human and mouse gene expression patterns based on normalized EST abundance in various normal and cancerous tissues.

ProdoNet

Sun, 13 May 2012 12:30:05 -0400

A web-based application for the mapping of prokaryotic genes and the corresponding proteins to common gene regulatory and metabolic networks. Users input a list of genes from which shared operons, co-expressed genes and shared regulators are detected. Common metabolic pathways are then viewed on KEGG maps.

mirConnX

Thu, 17 May 2012 20:40:07 -0400

mirConnX is a web server for inferring, displaying and parsing mRNA and microRNA gene regulatory networks. mirConnX combines sequence information with gene expression data analysis to create a disease specific, genome wide regulatory network. Only supports human and mouse.

CRSD

Sun, 20 May 2012 01:00:07 -0400

Composite Regulatory Signature Database (CRSD) is a microarray analysis pipeline aimed at the discovery of motifs involved in gene regulation including microRNA signatures and transcription factor binding sites (TFBS).

CARRIE

Fri, 18 May 2012 20:50:06 -0400

Server which analyzes microarray and promoter sequence data associated with a response to a specific stimulus. After analysis a potential transcriptional regulatory network is created. CARRIE also determines which transcription factors were likely involved in regulation and which genes they regulated.

INTERFEROME

Sat, 19 May 2012 15:30:05 -0400

INTERFEROME is an open access database of types I, II and III Interferon regulated genes collected from analysing expression data sets of cells treated with IFNs. This database integrates expression information with annotation, ontology, orthologue sequences from 37 species, tissue expression patterns and gene regulatory information.

CIBEX

Fri, 18 May 2012 22:50:06 -0400

The Center for Information Biology gene EXpression database (CIBEX) is a public repository for gene expression experimental data. The database system is compliant with the MIAME standard.

XenBase

Sun, 20 May 2012 08:40:10 -0400

Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. New content has been added including a section on gene expression patterns that incorporates image data from the literature, large scale screens and community submissions. Gene expression data are integrated into the gene catalog via an expression tab and is also searchable by multiple criteria using an expression search interface. Xenbase collaborates with the European Xenopus Research Center (EXRC) to provide a stock center section with data on frog lines supplied by the EXRC. Numerous improvements have also been made to search and navigation. Xenbase is also the source of the Xenopus Anatomical Ontology and for Xenopus gene nomenclature.

AutoClass@IJM

Mon, 21 May 2012 01:50:08 -0400

AutoClass is an unsupervised Bayesian classification system. AutoClass@IJM provides a web interface for this clustering algorithm.

COXPRESdb

Sun, 20 May 2012 05:10:08 -0400

COXPRESdb (coexpressed gene database) represents the coexpression relationship for human and mouse. Upgrades include a new comparable coexpression measure, Mutual Rank, five other animal species, rat, chicken, zebrafish, fly and nematoda, and addition of different layers of omics data into the integrated network of genes.

Bgee

Sat, 19 May 2012 20:00:09 -0400

Bgee is a dataBase for Gene Expression Evolution. It allows one to automatically compare gene expression patterns between species, by referencing expression data on anatomical ontologies, and designing homology relationships between them.

DEEP

Fri, 18 May 2012 23:00:05 -0400

DEEP (Differential Expression Effector Prediction) is a tool that can identify effectors of specific expression profiles by combining gene expression data with biological expert knowledge about biomolecular interaction networks (provided by resources like TRANSPATH, for example).

miRGator v2.0

Sun, 20 May 2012 22:40:05 -0400

miRGator is an integrated database of microRNA (miRNA)-associated gene expression, target prediction, disease association and genomic annotation for the functional investigation of miRNA. miRGator v2.0 contains information about : 1) Human miRNA expression profiles under various experimental conditions, 2) Gene expression profiles under miRNA-perturbation (e.g. miRNA knockout and overexpression), 3) Known and predicted miRNA targets, 4) MicroRNA-disease associations.

GeneMANIA

Wed, 16 May 2012 20:30:04 -0400

GeneMANIA is web interface for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays. Users input a query list for extension and weighting with functionally similar genes. Six organisms are supported.

BioMet Toolbox

Sun, 20 May 2012 12:40:10 -0400

The BioMet Toolbox consists of web-based resources for stoichiometric analysis of metabolic networks and for integration of transcriptome and interactome data into these networks to simulate growth rates, substrate uptake rates and metabolic production rates. Files for model organisms are included.

VisANT

Wed, 16 May 2012 03:20:08 -0400

VisANT is an integrative visual analysis tool for biological networks and pathways that contains modules for querying and integrating KEGG pathways with expression data. VisANT is java-based, and can be run as a java applet, as a java web application, or downloaded and run locally. New functions in VisANT 3.5 allow determination of over-representation and expression enrichment.

DiRE

Sun, 20 May 2012 09:30:04 -0400

A web server for predicting distant (outside of proximal promoter regions) regulatory elements (DiRE) in higher eukaryotic genomces using gene co-expression data, comparative genomics as well as transcription factor binding site information. DiRE allows users to start analysis with raw microarray expression data.

ArrayExpress update

Sat, 19 May 2012 11:40:09 -0400

The ArrayExpress Archive is a public repository of functional genomics data supporting publications. It includes data generated by sequencing or array-based technologies. Data are submitted by users and imported directly from the NCBI Gene Expression Omnibus. The ArrayExpress Archive is closely integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. Advanced queries provided via ontology enabled interfaces include queries based on technology and sample attributes such as disease, cell types and anatomy.

OPTIMIZER

Sat, 19 May 2012 11:30:09 -0400

OPTIMIZER is an application that optimizes the codon usage of a DNA sequence. This server can be used to predict and optimize the level expression of a gene in heterologous gene expression systems.

MADNet

Sat, 19 May 2012 18:40:09 -0400

Microarray Database Network (MADNet) is a data mining and visualization tool for analysis of diverse high-throughput biological data such as microarrays and phage display experiments. Data is integrated with information from NCBI, KEGG TRANSFAC and DrugBank.

Pscan

Thu, 17 May 2012 13:20:07 -0400

Pscan is a web server scans a set of sequences to find over-represented transcription factor binding site motifs within co-regulated or co-expressed genes.

g:Profiler

Thu, 17 May 2012 20:30:04 -0400

g:Profiler is a set of tools for functional annotation of gene lists that includes: g:GOSt, which retrieves the most significant Gene Ontology (GO) terms, KEGG and REACTOME pathways, and TRANSFAC motifs; g:Convert, for conversion between gene or protein names/IDs; g:Orth, for retrieving orthologs; and, g:Sorter, which searches for similar expression profiles. Functional analysis of SNPs and other DNA polymorphisms is also supported, as is enrichment analysis.

oPOSSUM

Thu, 17 May 2012 23:50:20 -0400

oPOSSUM is a web-based system for the detection of over-represented transcription factor binding sites in the promoters of sets of genes.

WikiGene

Sun, 20 May 2012 13:00:11 -0400

WikiGene is a scientific project that follows a community-based approach to collect data about genes and gene regulatory events.

Plant Resistance Genes database

Fri, 18 May 2012 06:30:14 -0400

PRGdb is a database provides a comprehensive overview of resistance genes (R-genes) in plants. PRGdb holds more than 16,000 known and putative R-genes belonging to 192 plant species challenged by 115 different pathogens and linked with useful biological information. Data can be examined using different query tools. A prediction pipeline called Disease Resistance Analysis and Gene Orthology (DRAGO), based on reference R-gene sequence data, was developed to search for plant resistance genes in public datasets such as Unigene and Genbank. The inferred cross-link between genomic and phenotypic information allows access to a large body of information.

GeneSeeker

Thu, 17 May 2012 09:20:09 -0400

GeneSeeker allows you to generate a list of candidate genes related to a human genetic disorder by searching against localization and expression databases.

POXO

Fri, 18 May 2012 22:30:16 -0400

POXO is a series of tools that can be used to discover, search and verify possible regulatory cis-element(s) from set(s) co-expressed genes.

CONFAC

Sun, 20 May 2012 09:20:08 -0400

The Conserved Transcription Factor Binding Site Finder (CONFAC) takes a list of human gene names and identifiers as input, and compares them with their mouse orthologues to identify conserved transcription factor binding sites. Further information from the user allows CONFAC to identify binding sites that are enriched in the promoter regions of gene clusters from microarray analyses when compared to control gene sets.

Pomelo II

Sat, 19 May 2012 18:00:10 -0400

Pomelo II is a web-server for the analysis of gene (and protein) expression and tissue array data. Different statistical tests are applied depending on the input data. Links are also provided to additional sources of information such as PubMed references, Gene Ontology terms, GO terms, etc.

VisHiC

Sun, 20 May 2012 11:10:05 -0400

VisHiC is a web server for clustering and compact visualization of gene expression data combined with automated function enrichment analysis. Output includes a heatmap of the expression matrix highlighting enriched clusters.

EMAGE

Sat, 19 May 2012 04:30:10 -0400

EMAGE is a freely available online database of in situ gene expression patterns in the developing mouse embryo. Gene expression domains from raw images are extracted and integrated spatially into a set of standard 3D virtual mouse embryos at different stages of development, which allows data interrogation by spatial methods. An anatomy ontology is also used to describe sites of expression, which allows data to be queried using text-based methods. Data coverage has been increased by sourcing from a greater selection of journals.

ToppGene Suite

Fri, 18 May 2012 02:30:11 -0400

ToppGene has a suite of tools for gene list functional enrichment, gene prioritization and identification of novel disease genes in an interactome.

ProfCom

Fri, 18 May 2012 01:50:13 -0400

Profiling of complex functionality (ProfCom) is a web based tool for the interpretation of genes that were identified to be functionally linked. Combinations of annotation terms are used to profile complex functions.

GOEAST

Sun, 20 May 2012 07:20:11 -0400

Gene Ontology Enrichment Analysis (GOEAST) is a toolkit for the identification of over-represented GO terms in a given gene set. Distinguishing features include: capacity to analyze data from various sources and from multiple species, and the capacity to cross compare GO enriched terms across experiments to identify correlations.

PAP

Sun, 20 May 2012 04:10:19 -0400

Promoter Analysis Pipeline (PAP) can identify potential transcriptional regulators for sets of co-expressed genes and identify potential regulatory targets of transcription factors.

POBO

Sun, 20 May 2012 17:30:07 -0400

POBO is a tool to summarize, verify and screen predetermined cis-element motifs from a set of sequences. POBO reports the results in as understandable format as possible for biologists.

INCLUSive

Sun, 20 May 2012 13:50:09 -0400

INCLUSive is a set of tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements.

WhichGenes

Fri, 18 May 2012 05:00:07 -0400

WhichGenes is a web based tool for gathering, building, storing and exporting gene sets with application to gene set enrichment analysis. The user may export a gene set in any desired output format with multiple gene identifiers.

GeneSeqer

Sun, 20 May 2012 20:50:06 -0400

GeneSeqer is a method to identify exon/intron structure by splice site prediction and spliced alignment in plant genomes.

KEGG: Kyoto Encyclopedia of Genes and Genomes

Thu, 17 May 2012 14:40:23 -0400

Pathway maps, molecular catalogs, genome maps and gene catalogs that capture knowledge about interactions in terms of information pathways. KEGG comprises several databases, including BRITE (protein-protein interactions), PATHWAY (interaction networks for cellular processes), and LIGAND (chemical compounds and chemical reactions). KEGG Atlas is a new tool for the global analysis of metabolic pathways.

GXA

Fri, 18 May 2012 12:50:06 -0400

The Gene Expression Atlas is an added-value database providing information about gene expression in different cell types, organism parts, developmental stages, disease states, sample treatments and other biological/experimental conditions. The content of this database derives from curation, re-annotation and statistical analysis of selected data from the ArrayExpress Archive of Functional Genomics Data. A simple interface allows the user to query for differential gene expression either (i) by gene names or attributes such as Gene Ontology terms, or (ii) by biological conditions, e.g. diseases, organism parts or cell types.

GoGene

Sun, 20 May 2012 12:00:09 -0400

GoGene performs high-throughput text mining to complement annotation of genes. GoGene supports search for genes in PubMed, EntrezGene and BLAST.

GenePattern 2.0

Mon, 21 May 2012 00:20:09 -0400

GenePattern combines a powerful scientific workflow platform with more than 100 genomic analysis tools. An intuitive web interface makes it easy to use.

Plant MicroRNA Database

Sun, 20 May 2012 17:30:08 -0400

The plant miRNA database (PMRD) integrates available plant miRNA data deposited in public databases, gleaned from the recent literature, and data generated in-house. This database contains sequence information, secondary structure, target genes, expression profiles and a genome browser. Includes model plants and major crops such as Arabidopsis, rice, wheat, soybean, maize, sorghum, barley, etc. For Arabidopsis, rice, poplar, soybean, cotton, medicago and maize, the possible target genes for each miRNA with a predicted interaction site are included in the database. In some instances, miRNA expression profiles are included in the PMRD.

MARQ

Thu, 17 May 2012 02:20:06 -0400

MARQ is a web based application that allows users to compare a query set of genes (query signature) against a gene signature database built from GEO datasets for different organisms and platforms.

BEARR

Sat, 19 May 2012 05:20:05 -0400

Batch Extraction and Analysis of cis-Regulatory Regions (BEARR) takes a list of gene identifiers (such as RefSeq and Unigene IDs), consensus patterns, and (optionally) a position weight matrix as input and returns a list of matches for the patterns in both the sense and anti-sense strands of the relevant genomic sequence. The user specifies what distance up and downstream from both the transcription start site and the 3\' terminus to look for the patterns.

Defining Transcriptional Programs in Vascular Endothelium

Sun, 20 May 2012 02:50:11 -0400

This website contains microarray analysis software (Argus and Z-pool), an Endothelial Cell Expression Database, and other resources related to Vascular Endothelium research. See the PubMed abstracts for more information.

TransFind

Fri, 18 May 2012 05:40:16 -0400

TransFind web server predicts transcription factor binding sites in promoter regions of co-regulated gene sets.

SAGE Home Page

Mon, 21 May 2012 03:20:08 -0400

Serial Analysis of Gene Expression; simultaneous expression and map information.

REDUCE

Mon, 21 May 2012 04:40:06 -0400

REDUCE uses a motif-based regression method for the identification of TFBS (transcription factor binding sites) from microarray data in yeast, worm and fly. A free registration is required.

bioNMF

Mon, 21 May 2012 04:00:09 -0400

A web-based tool based on nonnegative matrix factorization (NMF) that can be used to provide new information from multi-dimensional biological data sets.

Microarray Retriever

Wed, 16 May 2012 12:40:08 -0400

Microarray Retriever (MaRe) is a web tool that enables batch search and retrieval of microarray datasets matching user specified criteria from the data in GEO and ArrayExpress microarray repositories. Such batch download facilitates gene expression meta-analysis.

ArrayExpress

Sun, 20 May 2012 22:20:05 -0400

Public repository for microarray based gene expression data; contains several curated gene expression datasets.

TRANSFAC

Mon, 21 May 2012 03:30:08 -0400

Transcription Factor Database of eukaryotic cis-acting regulatory DNA elements and trans-acting factors; free for non-commercial use.

GEPAS

Sat, 19 May 2012 19:00:07 -0400

The Gene Expression Pattern Analysis Suite (GEPAS) is a collection of tools for the analysis of microarray data. GEPAS includes tools for data pre-processing, clustering, differential gene expression, predictors, array CGH and functional annotation. A new pipeline module allows for automation of sequential analysis steps.

PathExpress

Sat, 12 May 2012 02:40:06 -0400

PathExpress is a tool developed to interpret gene expression data obtained from microarray experiments by identifying and visualizing the most relevant metabolic pathways associated with a subset of genes (e.g. differentially expressed genes). Enzyme Neighborhood (a sub-network of linked enzymes with a limited path length) allows identification of the most relevant sub-network affected in a gene expression experiment.

The European Bioinformatics Institute (EBI)

Thu, 17 May 2012 23:10:17 -0400

The European Bioinformatics Institute (EMBL-EBI) provides access to a comprehensive, integrated set of biological data. Resources include information on genes, genomes, proteins, expression, literature, and molecular interactions as well as many other useful resources.

SOURCE

Sat, 19 May 2012 10:40:15 -0400

Stanford Online Universal Resource for Clones and ESTs pools publicly available data commonly sought for any clone, GenBank accession, or gene from human, mouse, rat.

OligoArray

Fri, 18 May 2012 20:10:04 -0400

OligoArray is free software that computes gene specific oligonucleotides for genome-scale oligonucleotide microarray construction. A database of pre-designed oligonucleotide microarray probes for organisms with a fully sequenced genome can be found at http://berry.engin.umich.edu/oligoarraydb/index.html

GenMAPP

Sun, 20 May 2012 18:30:09 -0400

GenMAPP (Gene MicroArray Pathway Profiler) is a microarray expression data visualization tool, allowing data to be viewed on maps representing gene groupings and biological pathways.

RuleGO

Thu, 17 May 2012 14:32:47 -0400

RuleGO is a web tool for description of gene groups by means of Gene Ontology. The user is able to describe gene groups on the basis of logical rules that include GO-terms in their premises.

ChipInfo

Mon, 21 May 2012 03:10:10 -0400

ChipInfo extracts gene annotation and gene ontology information from databases like NetAffx and Gene Ontology (GO) for microarray analysis. Output is provided in tabular format and the program is available for download for use on your own machine.

WebGestalt

Sun, 13 May 2012 09:20:13 -0400

WebGestalt (WEB-based GEne SeT AnaLysis Toolkit) is a system facilitating the analysis of sets of genes. Gene sets can be compared using set operations (intersection, union, etc.), different annotations can be selected and retrieved for the set, and sets can be visualized and organized by a user-selected method (Gene Ontology, chromosomal distribution, etc.). WebGestalt can also perform a statistical analysis to suggest areas of interest with respect to the set of genes selected.

BTW

Sat, 19 May 2012 21:00:06 -0400

Boltzmann Time Warping (BTW) computes time warping distances and Boltzmann\' pair probabilities for a given input gene expression time series. This tool helps to identify genes that may share similar expression patterns over time.

SAGEmap

Mon, 21 May 2012 03:10:11 -0400

SAGE tag to gene mapping by NCBI.

ENDEAVOUR

Sat, 19 May 2012 12:50:17 -0400

ENDEAVOUR is a computational approach to prioritize candidate genes for further study. Users input training genes already known to be involved in the process under study and the candidate genes to prioritize. The web server supports multiple species and integrates multiple genomic data to generate the final prioritization. ENDEAVOUR has been benchmarked in silico and experimentally validated leading to the discovery of novel disease genes in several genetic diseases.

PrimerBank

Sun, 20 May 2012 04:30:09 -0400

PrimerBank is a public resource for the retrieval of human and mouse primer pairs for gene expression analysis by PCR and Quantitative PCR (QPCR). Information on these primers such as T(m), location on the transcript and amplicon size is also included. For each gene, at least one primer pair has been designed and in many cases alternative primer pairs exist. Primers have been designed to work under the same PCR conditions, thus facilitating high-throughput QPCR. There are several ways to search for primers for the gene(s) of interest, such as by: GenBank accession number, NCBI protein accession number, NCBI gene ID, PrimerBank ID, NCBI gene symbol or gene description (keyword). Primer pairs covering most known mouse genes have been experimentally validated by QPCR, agarose gel analysis, sequencing and BLAST, and all validation data can be freely accessed from the PrimerBank web site.

DroID

Sun, 20 May 2012 09:30:06 -0400

DroID, the Drosophila Interactions Database, is a comprehensive public resource for Drosophila gene and protein interactions. DroID contains genetic interactions and experimentally detected protein-protein interactions curated from the literature and from external databases, and predicted protein interactions based on experiments in other species. Protein interactions are annotated with experimental details and periodically updated confidence scores. The database now includes transcription factor-gene and regulatory RNA-gene interactions. Orthologous gene mappings of Drosophila genes to other organisms are also available to facilitate finding interactions based on gene names and identifiers for a number of common model organisms and humans.

BioProspector

Thu, 17 May 2012 20:20:08 -0400

Server which scans upstream of genes in the same gene expression cluster for regulatory sequence motifs using a Gibbs sampling strategy. The Markov background model is used for non-motif bases, improving specificity of predicted motif locations.

ADGO

Sun, 20 May 2012 07:20:15 -0400

ADGO is a web tool that provides composite interpretations for microarray data comparing two sample groups. It also provides composite interpretations and enrichment analysis for lists of genes from diverse sources of biological information.

MedMiner

Fri, 18 May 2012 06:10:10 -0400

MedMiner can be used to select genes from a microarray set based on GeneCards information. Based on the genes selected one can then search PubMed abstracts using known gene synonyms and other user-specified search parameters. The PubMed search can also be done independently of a microarray gene set. Results are grouped based on a set of relational keywords.

PHIRE

Fri, 18 May 2012 21:20:05 -0400

Phage In silico Regulatory Elements (PHIRE) is a standalone program in Visual Basic which performs a string-based search on bacteriophage genome sequences discovering and extracting blocks displaying sequence similarity corresponding to conserved regulatory elements contained within these genomes.

GEMS

Sat, 19 May 2012 00:40:11 -0400

GEMS (Gene Expression Mining Server) is a tool for biclustering microarray data. It is available as a web tool and as a standalone command-line program.

PILGRM

Sun, 20 May 2012 15:00:25 -0400

The Platform for Interactive Learning by Genomics Results Mining (PILGRIM) is an interactive data driven discovery platform for biology. Expression levels of known relevant genes (specified by the user) are used to discover additional genes with similar expression patterns in large compendia of microarray data. By carefully defining the lists of relevant genes, the user controls the specificity of discoveries.

AMIC@

Fri, 18 May 2012 12:10:11 -0400

The All Microarray Clustering @ once (AMIC@) web application provides users with a range of microarray gene expression data clustering algorithms. Algorithms can be run concurrently on the same data sets. Data can be visualized by heat maps and downloaded as a standard clustered data file for further analysis.

mirAct

Sun, 20 May 2012 02:40:11 -0400

mirACT web server is a tool designed to investigate miRNA activity in gene expression data. It uses the negative regulation relationship between miRNAs and their target genes.

PANTHER Tools

Sun, 20 May 2012 04:40:04 -0400

The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function. The PANTHER research tools allow you to score proteins against the PANTHER HMM library, use PANTHER to do gene expression analyses, and download PANTHER tools and data.

ChIP-Array

Sun, 20 May 2012 08:10:18 -0400

ChIP-Array is a web server that integrates ChIP-seq and microarray gene expression data to discover direct and indirect target genes regulated by a transcription factor of interest.

BiologicalNetworks

Fri, 18 May 2012 14:20:10 -0400

BiologicalNetworks allows retrieval, construction, and visualization of biological networks and allows for the analysis of high-throughput expression data by mapping onto network graphs. BiologicalNetworks queries the PathSys system, a combined database of biological pathways, gene regulatory networks, and protein interaction maps.

T-profiler

Sun, 13 May 2012 09:10:11 -0400

T-profiler is a tool for the analysis of gene expression data from yeast that uses the t-test to score changes in the average activity of pre-defined groups of genes.

ACT

Sun, 20 May 2012 04:00:08 -0400

Arabidopsis Co-expression Tool (ACT) is a resource for investigating the co-expression of genes in the NASC/GARNet microarray-based gene expression dataset from Arabidopsis.

GFINDer

Sun, 20 May 2012 21:00:05 -0400

Genome Functional INtegrated Discoverer (GFINDer) takes a list of gene/clone IDs with classification information as input, and allows the user to characterize the different gene classes in the list using annotations of various types from several different sources.

RACE

Sat, 19 May 2012 19:20:07 -0400

RACE (Remote Analysis Computation for gene Expression data) is a collection of web tools designed to assist with the analysis of DNA microarray data and results.

PEACE

Sat, 19 May 2012 19:30:05 -0400

Parallel Environment for Assembly and Clustering of Gene Expression (PEACE) web tool performs high-throughput ab initio clustering of transcript fragment sequences from next-generation sequencing platforms.

GraphWeb

Fri, 18 May 2012 23:00:04 -0400

GraphWeb is a web server for biological network analysis and module design using a graphical interface.

AGRIS

Sat, 19 May 2012 14:40:10 -0400

The Arabidopsis Gene Regulatory Information Server (AGRIS) provides a comprehensive resource for gene regulatory studies in the model plant Arabidopsis thaliana. Three interlinked databases, AtTFDB, AtcisDB and AtRegNet, furnish comprehensive and updated information on transcription factors (TFs), predicted and experimentally verified cis-regulatory elements (CREs) and their interactions, respectively.

ConsensusPathDB

Mon, 14 May 2012 23:20:05 -0400

ConsensusPathDB is a meta-database that integrates physical protein interactions, metabolic and signaling reactions and gene regulatory interactions in a seamless functional association network that simultaneously describes multiple functional aspects of genes, proteins, complexes, metabolites, etc. ConsensusPathDB offers different ways of utilizing these integrated interaction data, with tools for visualization, analysis and interpretation of high-throughput expression data in the light of functional interactions and biological pathways.

Quadruplex

Sat, 19 May 2012 19:00:13 -0400

A website to serve the quadruplex community. Contains conference information, forums, database and parsers.

PlnTFDB

Wed, 16 May 2012 10:40:05 -0400

The Plant Transcription Factor Database (PlnTFDB) is an integrative database that provides putatively complete sets of transcription factors (TFs) and other transcriptional regulators (TRs) in plant species whose genomes have been completely sequenced and annotated. For each gene family, a basic description is provided that is complemented by literature references, and multiple sequence alignments of protein domains. TF or TR gene entries include information of expressed sequence tags, 3D protein structures of homologous proteins, domain architecture and cross-links to other computational resources online. Moreover, the different species in PlnTFDB are linked to each other by means of orthologous genes facilitating cross-species comparisons.

KaPPA-View4

Mon, 21 May 2012 05:10:03 -0400

KaPPA-View4 is a metabolic pathway database which is able to overlay gene-to-gene and/or metabolite-to-metabolite relationships as curves on a metabolic pathway map, or on a combination of up to four maps. Pathway maps of the Kyoto Encyclopedia of Genes and Genomes (KEGG) and maps generated from their gene classifications are available at KaPPA-View4 KEGG version. Gene co-expression data from the databases ATTED-II, COXPRESdb, CoP and MiBASE for human, mouse, rat, Arabidopsis, rice, tomato and other plants are available.

dbDEPC

Mon, 21 May 2012 00:10:09 -0400

A database of differentially expressed proteins in human cancers (dbDEPC) collects curated cancer proteomics data, provides a resource for information on protein-level expression changes, and explores protein profile differences among different cancers. dbDEPC currently contains 1803 proteins differentially expressed in 15 cancers, curated from 65 mass spectrometry (MS) experiments in peer-reviewed publications.

MDscan

Sat, 19 May 2012 04:30:04 -0400

Server designed to pinpoint protein-DNA interaction sites at the base pair level. Uses ChIP-array data, word enumeration and position-specific weight matrix updating to search for motifs representing these interaction sites.

Onto-Tools

Mon, 21 May 2012 03:00:09 -0400

Onto-Tools is a suite of tools for data mining based on information from Gene Ontology (GO). Onto-Tools includes an annotation database and the data mining tools: Onto-Express, Onto-Compare, Onto-Design, Onto-Translate, Onto-Miner, Pathway-Express, Promoter-Express, nsSNPCounter, TAQ, and OE2GO; free registration is required.

PlnTFDB

Sun, 20 May 2012 12:50:04 -0400

Plant Transcription Factor Database (PlantTFDB) is database that attempts to identify a comprehensive set of plant genes coding for transcription factors. A web interface to the database allows users to browse by species, search using a sequence identifier, or query using BLAST.

JProGO

Sun, 20 May 2012 19:40:11 -0400

JProGO is a tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information.

Pathway Explorer

Sun, 20 May 2012 22:00:04 -0400

Pathway Explorer is a tool for visualizing high throughput expression data simultaneously with biological pathway data available from KEGG, BioCarta, and GenMAPP.

PINTA

Sun, 20 May 2012 00:10:11 -0400

PINTA is a web tool for the prioritization of candidate genes based on the differential expression of their neighborhood in a genome-wide protein-protein interaction network. PINTA is available for 5 species (human, mouse, rat, worm and yeast).

SEA

Fri, 18 May 2012 14:40:31 -0400

Serial Expression Analysis (SEA) suite of tools provides a complete resource for the analysis of serial transcriptomic data.

KARMA

Fri, 18 May 2012 11:00:13 -0400

KARMA (Keck Array Manager and Annotator) allows you compare and annotate your own microarrays against other available arrays. Comparison of arrays can be achieved within the same species as well as across species (array comparison is based on UniGene Cluster ID and/or Homologene data). Annotation data includes LocusLink, SwissProt, and Gene Ontology.

DIANA-microT

Sun, 20 May 2012 14:40:12 -0400

The DIANA-microT web server predicts targets for miRNAs and provides functional information on the predicted miRNA:target gene interaction from various online biological resources. Updates enable the association of miRNAs to diseases through bibliographic analysis and connection to the UCSC genome browser.

MAGMA

Sun, 20 May 2012 13:10:11 -0400

MAGMA can be used for the analyses of two-channel microarray experiments and computes genes with significant differential expression using R and Bioconductor. Automatically generated R-scripts are available for download.

Affymetrix NetAffx Analysis Center

Mon, 21 May 2012 01:30:10 -0400

Allows correlation of GeneChip array results with array design and annotation information; provides access to array content information, including probe sequences and gene annotations; free registration is required.

AltAnalyze

Sun, 20 May 2012 08:50:08 -0400

AltAnalyze is a comprehensive tool for the analysis of gene expression and alternative splicing data from RNA-seq and Affymetrix (exon, gene, junction) datasets at the level of proteins, domains, microRNA binding sites and pathways. The Cytoscape plugin DomainGraph (www.domaingraph.de) allows for visualization of AltAnalyze results at multiple levels of abstraction (e.g., isoform, exon, protein, domain, molecular interactions).

RegulonDB

Fri, 18 May 2012 09:20:11 -0400

RegulonDB is a reference database of Escherichia coli K-12. Transcriptional regulation is now part of a unit that initiates with the signal and continues with the signal transduction to the core of regulation, modifying expression of the affected target genes responsible for the response. RegulonDB has summaries for every transcription factor (TF) and TF-binding sites with internal symmetry. In addition to data from the literature, we have incorporated our own information on transcription start sites (TSSs) and transcriptional units (TUs), obtained by using high-throughput whole-genome sequencing technologies. A new portable drawing tool for genomic features is also now available, as well as new ways to download the data, including web services, files for several relational database manager systems and text files including BioPAX format.

Patrocles

Fri, 18 May 2012 23:20:11 -0400

The Patrocles database compiles DNA sequence polymorphisms (DSPs) that are predicted to perturb miRNA-mediated gene regulation.

GenoCAD

Sat, 19 May 2012 04:30:06 -0400

GenoCAD is a web-based application for designing protein expression vectors, artificial gene networks and other genetic constructs composed of multiple functional blocks. Users can download the designed sequence for synthesis or further analysis. Users can also create personal accounts and thus can customize their workspace.

MIDAW

Sun, 20 May 2012 03:20:07 -0400

MIDAW (MIcroarray Data Analysis Web tool) is a data normalization and analysis tool for microarray data.

Stanford Microarray Database (SMD)

Mon, 21 May 2012 05:00:10 -0400

SMD stores raw and normalized data from microarray experiments, as well as their corresponding image files. In addition, SMD provides interfaces for data retrieval, analysis and visualization.

CREME

Wed, 16 May 2012 02:10:06 -0400

CREME (Cis-Regulatory Module Explorer for the human genome) is a tool for identifying and visualizing cis-regulatory modules for a given set of genes that are potentially co-expressed or co-regulated. It takes as input a list of accession numbers, and reports back common modules, grouping genes from the list by which modules are found in their promoter regions.

Web Weeder

Wed, 16 May 2012 14:00:09 -0400

Server which identifies conserved motifs within sets of related regulatory DNA sequences, which are likely to be transcription factor binding sites. The interface will automatically conduct several runs using different parameters and output a summary.

MIAMExpress

Thu, 10 May 2012 00:30:36 -0400

MIAME (minimum information about a microarray experiment) compliant microarray data submission tool.

ArrayPipe

Sun, 20 May 2012 21:10:03 -0400

ArrayPipe allows users to customize a processing pipeline for the analysis of microarray data. Includes methods for quality assessment of slides, data visualization, normalization, and detection of differentially expressed genes. Output consists of reports formatted as standard web pages and tab-delimited lists of calculated values.

CARMAweb

Sun, 20 May 2012 18:20:10 -0400

Comprehensive R based Microarray Analysis web service (CARMAweb) is a resource for the analyses of microarray data including data preprocessing, detection for differentially expressed genes, cluster analysis, and GO analysis. Calculations are performed in R using functions provided by BioConductor.

ORegAnno

Sun, 20 May 2012 23:50:09 -0400

The Open REGulatory ANNOtation database (ORegAnno) is a collection of literature-curated regulatory regions, transcription factor binding sites (TFBS) and regulatory mutations.

DAVID Bioinformatics Resources

Sun, 20 May 2012 06:10:13 -0400

The Database for Annotation, Visualization and Integrated Discovery (DAVID) provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes.

ASPic

Sun, 20 May 2012 15:40:09 -0400

Alternative Splicing Prediction (ASPic) can predict alternative splicing of user submitted genes based on comparative analysis of available transcript and genome data from a variety of species. Results include graphical and tabular views of the splicing patterns of full-length mRNA isoforms compatible with the detected splice sites of the genes as well as structural and functional annotations.

T-Reg Comparator

Sun, 20 May 2012 21:40:06 -0400

T-Reg Comparator is a tool for the analysis of transcriptional regulation that allows you to compare a set of position weight matrices (PWM) against the T-Reg database (a collection of PWMs built from Transfac and Jaspar).

WordSpy

Sat, 19 May 2012 03:20:07 -0400

WordSpy allows the user to search for over-represented words in a set of sequences and to search for discriminative words using negative sequence data. WordSpy employs this functionality as a means to search for transcription factor binding motifs.

Phyloscan

Sat, 19 May 2012 06:40:08 -0400

Phyloscan is a web server that locates transcription regulating binding sites by exploiting binding site evolutionary conservation and repeats in promoter regions. Mixed aligned and unaligned sequence data may be used.

ExpressYourself

Tue, 15 May 2012 12:40:14 -0400

ExpressYourself is a web-based platform to process microarray data. It includes tools for background correction, normalization, data processing and filtering.

PaLS

Wed, 16 May 2012 06:40:05 -0400

Pathway and Literature Strainer (PaLS) highlights those members on a user inputted list that share descriptors from PubMed, GO, KEGG and Reactome.

CLIC

Sat, 19 May 2012 05:20:05 -0400

CLIC performs clustering analysis of large microarray datasets. Genes are first clustered in individual dimensions and then using the ordinal labels of clusters for each dimension, full dimension wide clustering is performed.

ArrayXPath

Sun, 20 May 2012 13:10:07 -0400

ArrayXPath is a web-based service for matching microarray gene-expression profiles with known biological pathways. Input is a clustered gene-expression profile in a tab-delimited text format. Output includes pathway diagrams.

POCO

Mon, 21 May 2012 03:30:06 -0400

POCO searches a set of promoters from co-expressed genes for nucleotide patterns that are over-represented.

Footer

Sat, 19 May 2012 20:50:12 -0400

Footer is a tool for identifying highly-probable binding sites of known transcription factors using phylogenetic footprinting principles to analyse two homologous DNA sequences.

Doelan

Sun, 20 May 2012 11:30:07 -0400

Doelan is an tool designed to monitor the quality of DNA microarray production.

PromoterPlot

Fri, 18 May 2012 18:50:08 -0400

PromoterPlot takes the output from a TransFac search as input, and finds similarities between groups of promoters in an attempt to simplify the results of transcription factor searches. FASTA/Affymetrix IDs can also be used as input for a local installation of the tool.

rQuant.web

Fri, 18 May 2012 12:10:04 -0400

rQuant.web is a web service for quantitative analysis of RNA sequencing data based on quadratic programming. rQuant.web is available as a tool in Galaxy.

OSU Bioinformatics and Computational Biology

Sun, 20 May 2012 13:10:08 -0400

The website of the Ohio State University Human Cancer Genetics Bioinformatics group. This site has many resources, including databases of promoters and transcription factors, software tools to predict potential P53 consensus binding sites and to predict first exon and promoter regions and a software toolkit for developing web-based applications to view genomic data.

SynoR

Sat, 19 May 2012 14:00:11 -0400

SynoR searches vertebrate genomes for synonymous regulatory elements.

Target Explorer

Sun, 20 May 2012 08:40:09 -0400

Target Explorer can be used to create custom matrices to describe transcription factor binding sites (TFBS), search for clusters of TFBS, and identify target genes. Free registration is required.

RibEx

Thu, 17 May 2012 21:20:11 -0400

Riboswitch Explorer (RibEx) searches sequences for known riboswitches and also for predicted bacterial regulatory elements that are highly conserved

MoD Tools

Mon, 21 May 2012 04:50:04 -0400

Tools for Motif Discovery (MoD) in nucleotide sequences that includes: Weeder, a program for detecting transcription factor binding sites (TFBS) in coregulated genes; WeederH, a tool for detecting TFBS and regulatory regions from homologous genes; and RNA profile, a tool for secondary structure motif discovery in RNA sequences.

ARGO

Sat, 19 May 2012 10:00:06 -0400

ARGO is a tool for the detection and visualization of sets of region-specific degenerate oligonucleotide motifs in the regulatory regions of eukaryotic genes.

OligoWiz

Mon, 21 May 2012 04:50:11 -0400

OligoWiz 2.0 is a client for microarray probe design that allows for the integration of sequence annotations, probe quality parameters, and the placement of multiple probes per transcript.

mirTools

Thu, 17 May 2012 01:30:05 -0400

mirTools allows users to comprehensively characterize the small RNA transcriptome from high-throughput sequencing data. Users can filter quality reads, align short reads to the reference genome, classify small RNA candidates into known miRNAs, non-coding RNA, genomic repeats, etc. among other analysis tools.

CoPub

Sat, 19 May 2012 17:40:11 -0400

CoPub is a text mining tool for the detection of biomedical terms that co-occur in abstracts with the list of input genes (human, rat, and mouse genes). CoPub also graphically displays differentially expressed genes and over-represented keywords in a network for better visualization of relationships. CoPub 5.0 uses a new thesauri. It allows for searching of keywords, provides highlighting and sorting mechanisms and statistics. It also searches for indirect relations between genes, pathways, drugs and diseases.

ProbeLynx

Mon, 21 May 2012 03:00:06 -0400

Using current releases of genomic sequence data, ProbeLynx allows users to assess the specificity of probe sequences used for microarray experiments. The user provides probe sequences in FASTA or tab-delimited format, and ProbeLynx reports specificity information for each probe and functional annotations from Ensembl or TIGR for each probe target hit.

CisMols

Sat, 19 May 2012 02:50:04 -0400

CisMols (Cis-regulatory Modules) is a tool that identifies compositionally predicted cis-clusters that occur in groups of co-regulated genes within each of their ortholog-pair evolutionarily conserved cis-regulatory regions.

NCBI GEO

Sun, 20 May 2012 03:00:12 -0400

The Gene Expression Omnibus (GEO) database stores over 20,000 microarray- and sequence-based functional genomics studies, and continues to handle the majority of direct high-throughput data submissions from the research community. Multiple mechanisms are provided to help users effectively search, browse, download and visualize the data at the level of individual genes or entire studies.

EcoCyc

Sun, 20 May 2012 04:10:07 -0400

EcoCyc is a comprehensive model organism database for Escherichia coli K-12 MG1655. From the scientific literature, EcoCyc captures the functions of individual E. coli gene products; their regulation at the transcriptional, post-transcriptional and protein level; and their organization into operons, complexes and pathways. EcoCyc users can search and browse the information in multiple ways. New features include combined gene/protein pages and a Regulation Summary Diagram displaying a graphical overview of all known regulatory inputs to gene expression and protein activity.

Cytoscape

Sat, 19 May 2012 02:40:09 -0400

Cytoscape is a visualization platform for use with molecular interaction networks. Interaction data can be integrated with other state data such as gene expression profiles. The input to Cytoscape includes lists of interaction pairs, and tab/space delimited files containing mRNA expression profiles. The nodes of the interaction networks can be filtered by such variables as GO annotations and number of interactions.

Génie

Sat, 19 May 2012 07:50:04 -0400

Genie evaluates the literature attached to all genes in a genome and to their orthologs for a selected topic. Hundreds of species and millions of genes are supported. Running times range from a few seconds to a minute in most of the cases.

MicrobesOnline

Sat, 19 May 2012 15:20:12 -0400

MicrobesOnline portal includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms. MicrobesOnline includes a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree. To identify co-regulated genes, MicrobesOnline can search for genes based on their expression profile, and provides tools for identifying regulatory motifs and seeing if they are conserved. MicrobesOnline also includes fast phylogenetic profile searches, comparative views of metabolic pathways, operon predictions, a workbench for sequence analysis and integration with RegTransBase and other microbial genome resources.

T1DBase

Sat, 19 May 2012 02:40:06 -0400

T1DBase is a database for type 1 diabetes (T1D). It integrates genetic, genomic and expression data relevant to T1D research across mouse, rat and human and presents this to the user as a set of web pages and tools. New data sets include curated summary data from four genome-wide association studies relevant to T1D, HaemAtlas-a data set and tool to query gene expression levels in haematopoietic cells and a manually curated table of human T1D susceptibility loci, incorporating genetic overlap with other related diseases.

Laminin database

Sat, 19 May 2012 14:10:09 -0400

The Laminin(LM)-database is a database focusing on the non-collagenous extracellular matrix protein family, the LMs. The homepage is subdivided into LMs, receptors, extracellular binding and other related proteins. Each tab opens into a given LM or LM-related molecule, where the reader finds a series of further tabs for 'protein', 'gene structure', 'gene expression' and 'tissue distribution' and 'therapy'. Data are separated as a function of species, comprising Homo sapiens, Mus musculus and Rattus novergicus.

CompareProspector

Sun, 20 May 2012 21:10:05 -0400

Server which attempts to identify any motifs related to genes predicted to share regulatory elements. It alters Gibbs sampling through biasing searches towards conserved sequences across multiple species.

FatiGOplus

Sun, 20 May 2012 15:20:05 -0400

FatiGOplus is a tool for the functional profiling of genome-scale experiments oriented to the interpretation of microarray experiments. As part of the Babelomics suite, FatiGOplus finds differential distributions of biological terms (GO, KEGG pathways, Interpro motifs, Transfac motifs, CisRed motifs, etc.) between two groups of genes.

CMA

Sat, 19 May 2012 20:40:06 -0400

Composite Module Analyst (CMA) defines promoter models based on the composition of transcription factor binding sites (TFBS) in regulatory sequences for sets of coregulated genes.

Ensembl Genomes

Sun, 20 May 2012 21:00:06 -0400

Ensembl Genomes is a new portal offering integrated access to genome-scale data from non-vertebrate species of scientific interest, developed using the Ensembl genome annotation and visualisation platform. Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. Data types incorporated include annotation of (protein and non-protein coding) genes, cross references to external resources, and high throughput experimental data (e.g. data from large scale studies of gene expression and polymorphism visualised in their genomic context). Additionally, extensive comparative analysis has been performed, both within defined clades and across the wider taxonomy, and sequence alignments and gene trees resulting from this can be accessed through the site.

CCancer

Wed, 16 May 2012 18:40:07 -0400

CCancer is an automatically collected database of gene lists reported in various studies. The current coverage is 3369 gene lists from 2644 papers. Enrichment analysis reports intersecting gene lists with an inputted gene list.

Zinc Finger Tools

Fri, 18 May 2012 20:10:08 -0400

Zinc Finger Tools provides several tools for selecting zinc finger protein target sites and for designing the proteins that will target them.

ENCODE DCC

Fri, 18 May 2012 19:20:07 -0400

The ENCODE project has a goal of cataloguing all the functional elements in the human genome. The ENCODE Data Coordination Center (DCC) serves as the central repository for ENCODE data. The DCC contains a collection of high-throughput, genome-wide data generated with technologies such as ChIP-Seq, RNA-Seq, DNA digestion and others. It includes sequences with quality scores, alignments, signals calculated from the alignments, and in most cases, element or peak calls calculated from the signal data. Each data set is available for visualization and download via the UCSC Genome Browser. ENCODE data can also be retrieved using a metadata system that captures the experimental parameters of each assay.

NeAT

Sat, 19 May 2012 02:20:05 -0400

Network Analysis Tools (NeAT) is a suite of tools for the analysis of biological networks, clusters, classes and pathways. Tools are available as web services for integration into programmatic work flows.

Cyclebase

Thu, 17 May 2012 15:20:19 -0400

Cyclebase is an online resource of cell-cycle-related experiments. This database provides an easy-to-use web interface that facilitates visualization and download of genome-wide cell-cycle data and analysis results. Data from different experiments are normalized to a common timescale and are complimented with key cell-cycle information and derived analysis results. Included is information on cyclin-dependent kinase (CDK) substrates, predicted degradation signals and loss-of-function phenotypes from genome-wide screens. The web interface provides a single, gene-centric graph summarizing the available cell-cycle experiments. Links to orthologous and paralogous genes are included to further facilitate comparison of cell-cycle regulation across species.

NCBI Resources

Sun, 20 May 2012 03:10:08 -0400

The National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site.

Cancer Genome Anatomy Project

Sun, 20 May 2012 07:10:11 -0400

Goal is to determine the gene expression profiles of normal, precancer, and cancer cells; resources for human and mouse include ESTs, gene expression patterns, SNPs, cluster assemblies, cytogenetic information, and tools to query and analyze the data.

ZFIN

Mon, 21 May 2012 00:40:05 -0400

ZFIN, the Zebrafish Model Organism Database serves as the central repository and web-based resource for zebrafish genetic, genomic, phenotypic and developmental data. ZFIN manually curates comprehensive data for zebrafish genes, phenotypes, genotypes, gene expression, antibodies, anatomical structures and publications. A wide-ranging collection of web-based search forms and tools facilitates access to integrated views of these data promoting analysis and scientific discovery. Data formats include text, images and graphical representations.

Bioverse

Fri, 18 May 2012 19:40:10 -0400

Bioverse is a system that uses computational techniques to facilitate exploring the relationships between molecular, genomic, proteomic, systems and organismal information.

FGDB

Sun, 20 May 2012 21:50:07 -0400

The MIPS Fusarium graminearum Genome Database (FGDB) is a comprehensive genome database for Fusarium graminearum. The current version of FGDB v3.1 provides information on the full manually revised gene set based on the Broad Institute assembly FG3 genome sequence. The database serves as a convenient entry point to explore expression data results and to obtain information on the Affymetrix GeneChip probe sets.

DyNAVacS

Thu, 17 May 2012 18:10:07 -0400

DyNAVacS is a tool for designing DNA vaccines that includes steps for chosing a suitable expression vector, ensuring optimal expression by codon optimization, engineering CpG motifs for enhancing immune responses, and providing additional sequence signals for efficient translation. It also allows includes restriction enzyme mapping and design of primers spanning user specified sequences.

Tomato Functional Genomics Database

Thu, 17 May 2012 20:00:05 -0400

Tomato Functional Genomics Database (TFGD) provides a comprehensive resource to store, query, mine, analyze, visualize and integrate large-scale tomato functional genomics data sets. Computational pipelines have been developed to process microarray, metabolite and sRNA data sets archived in the database, and TFGD provides downloads of all the analyzed results. TFGD is also designed to enable users to easily retrieve biologically important information through a set of efficient query interfaces and analysis tools, including improved array probe annotations as well as tools to identify co-expressed genes, significantly affected biological processes and biochemical pathways from gene expression data sets and miRNA targets, and to integrate transcript and metabolite profiles, and sRNA and mRNA sequences.

Pseudomonas Genome Project

Mon, 21 May 2012 03:00:04 -0400

This is a comprehensive database on all Pseudomonas species genomes providing primarily access to Pseudomonas aeruginosa genomic data and annotation. Its interface faciliates comparative analyses of genes, proteins, annotations and gene orders, and contains a wealth of additional data including pathway-based, operon-based, protein-localization based, gene function category and ortholog/paralog-based information.

MMIA

Sat, 19 May 2012 23:30:07 -0400

microRNA and mRNA Integrated Analysis (MMIA) is a web server that integrates miRNA and mRNA expression data with predicted miRNA target information. MMIA incorporates miRNA prediction algorithms (TargetScan, PITA, PicTar).

IBM Bioinformatics and Pattern Discovery Group

Sat, 19 May 2012 22:10:11 -0400

Extensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also exist on this server. A detailed help page is provided for all tools.

BioProfiling.de

Thu, 17 May 2012 14:32:13 -0400

BioProfiling.de provides a toolkit for the interpretation of gene or protein lists using enrichment of network based statistical frameworks.

R spider

Sun, 20 May 2012 02:00:03 -0400

R spider is a web tool for the analysis of a gene list using the systematic knowledge of core pathways and reactions from KEGG and Reactome.

AthaMap

Sat, 19 May 2012 22:00:04 -0400

AthaMap is a genome-wide map of putative transcription factor binding sites in Arabidopsis thaliana

Reactome

Wed, 16 May 2012 18:50:03 -0400

Reactome is a database of human biological pathways and processes ranging from basic processes of metabolism to complex regulatory pathways. The data is curated by biologists and subsequently peer-reviewed for accuracy and consistency. Cross-references with UniProt, PubMed, Ensembl, Gene Ontology and LocusLink are also provided. Reactome supersedes The Genome Knowledgebase project.

rSNP_Guide

Sun, 20 May 2012 19:10:04 -0400

a system of databases documenting the influence of mutations in regulatory gene regions

NBRP resources

Mon, 21 May 2012 03:10:06 -0400

The National BioResource Project (NBRP) is a system for collecting, preserving and providing bioresources for use as experimental materials for life science research. Thirty databases and an integrated database-retrieval system (BioResource World: BRW) have been created. BRW provides access to a collection of 4.5-million records on bioresources including wild species, inbred lines, mutants, genetically engineered lines, DNA clones, etc. BRW supports summary browsing, keyword searching, and searching by DNA sequences or gene ontology. The results of searches provide links to online requests for distribution of research materials.

JCat

Thu, 17 May 2012 20:10:08 -0400

JCAT (Java Codon Adaptation Tool) is a tool that can adjust the codon usage of an input sequence to the selected organism. Useful for improving the expression of foreign genes in hosts with different codon usage.

YEASTRACT

Sun, 20 May 2012 15:10:07 -0400

The YEAst Search for Transcriptional Regulators And Consensus Tracking (YEASTRACT) is a curated repository of regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae. YEASTRACT includes DISCOVERER, a set of tools that can be used to identify complex motifs found to be over-represented in the promoter regions of co-regulated genes. EASTRACT allows the identification of documented or potential transcription regulators of a given gene and of documented or potential regulons for each transcription factor. It also renders possible the comparison between DNA motifs and the transcription factor binding sites described in the literature. YEASTRACT provides a set of queries to search and retrieve important biological information from the gathered data and to predict transcription regulation networks in yeast from data emerging from gene-by-gene analysis or global approaches.

starBase

Sat, 19 May 2012 12:20:05 -0400

StarBase (sRNA target Base) facilitates the comprehensive exploration of miRNA-target interaction maps from CLIP-Seq and Degradome-Seq data. Two web servers are provided to discover novel miRNA target sites from CLIP-Seq and Degradome-Seq data. Our web implementation supports diverse query types and exploration of common targets, gene ontologies and pathways.

BioCyc Knowledge Library

Sat, 19 May 2012 17:00:04 -0400

BioCyc is a collection of pathway/genome databases derived either from the literature (EcoCyc and MetaCyc) or computationally (ie. HumanCyc). EcoCyc is used to visualize gene layout, biochemical reactions, and pathways for the E. coli chromosome; MetaCyc contains the enzymes, reactions, and pathways for a variety of organisms (mostly micro-organisms)

phiSITE

Wed, 16 May 2012 16:00:13 -0400

phiSITE is a database of gene regulation in bacteriophages. It collects experimentally confirmed or predicted regulatory elements (promoters, operators, terminators and attachment sites) from bacteriophages belonging to Siphoviridae, Myoviridae and Podoviridae families. The database is manually curated, the data are collected mainly form scientific papers, cross-referenced with other database resources (EMBL, UniProt, NCBI taxonomy database, NCBI Genome, ICTVdb, PubMed Central).

HHMD

Thu, 17 May 2012 05:40:11 -0400

Human Histone Modification Database (HHMD) focuses on the storage and integration of histone modification datasets that were obtained from laboratory experiments. HHMD incorporates 43 location-specific histone modifications in human. HHMD can be searched by histone modification, gene ID, functional categories, chromosome location and cancer name. HHMD also includes a user-friendly visualization tool named HisModView, by which genome-wide histone modification map can be shown.

CIPRO 2.5

Sat, 19 May 2012 20:50:10 -0400

The Ciona intestinalis protein database (CIPRO) is an integrated protein database for the tunicate species C. intestinalis. The CIPRO database collects published data as well as unique information from unpublished experimental data, such as 3D expression profiling, 2D-PAGE and mass spectrometry-based large-scale analyses at various developmental stages, curated annotation data and various bioinformatic data. Homologs in humans and major model organisms are included. Annotations are open to evaluation by users through the CIPRO website.

ResponseNet

Thu, 17 May 2012 14:32:32 -0400

ResponseNet is a network optimization approach for revealing signaling and regulatory networks linking genetic and transcriptomic screening data. Users upload weighted lists of proteins and genes.

TFM-Explorer

Sat, 19 May 2012 03:10:05 -0400

TFM-Explorer web server is a toolbox for the identification of putative transcription factor binding sites within a set of upstream regulatory sequences for a given set of genes. Only for human, mouse, rat, chicken and drosphila.

CEAS

Wed, 16 May 2012 17:40:05 -0400

Cis-regulatory Element Annotation System (CEAS) is a resource for ChIP-chip analyses that retrieves repeat-masked genomic sequences, calculates GC content, plots evolutionary conservation, maps nearby genes, and identifies enriched transcription factor binding (TFBS) motifs.

SCOPE

Sun, 20 May 2012 03:40:08 -0400

SCOPE (Suite for Computational identification Of Promoter Elements) is a set of programs aimed at identifying novel cis-regulatory elements from groups of upstream sequences. SCOPE does not have any nuisance parameters so does not require the user to guess what the results might be. SCOPE is also very robust to noisy data and is still 50% as accurate even in the presence of 4-fold noise. SCOPE can also identify other genes in the genome that might be coregulated with the original gene set.

DiscoverySpace

Sun, 03 Oct 2010 00:43:28 -0400

DiscoverySpace is a tool for gene expression analyses and biological discovery.

ALGGEN

Sat, 19 May 2012 07:10:11 -0400

ALLGEN server provides various tools for multiple sequence alignments, clustering, and assembly of ESTs. It also includes search tools for transcription factor binding sites (TFBS), repeated patterns, and transposons.

Bioconductor

Fri, 18 May 2012 22:20:11 -0400

Bioconductor is an open source and open development software project that aims to provide access to a wide range of powerful statistical and graphical methods for the analysis of genomic data.

Asterias

Sat, 19 May 2012 10:50:15 -0400

Asterias is a set of tools for the analyses of high throughput genomic data that includes applications for microarray data normalization, filtering, detection of differential gene expression, class and survival prediction model building, and analysis of array CGH data. Most applications use parallel computing resulting in significant increases in speed.

MYBS

Mon, 21 May 2012 00:20:07 -0400

MYBS (Mining Yeast Binding Sites) is a tool for mapping Transcription factors (TFs) and their binding sites (TFBSs) that integrates both experimentally verified (ChIP-chip data) and predicted position weight matrixes (PWMs) from several databases.

AUGUSTUS

Fri, 18 May 2012 09:20:10 -0400

AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface, or downloaded and run locally.

RegAnalyst

Mon, 14 May 2012 13:40:10 -0400

RegAnalyst is a web server that integrates MoPP (Motif Prediction Program), MyPatternFinder and MycoRegDB (mycobacterial promoter and regulatory elements database).

TROD

Sun, 20 May 2012 05:10:12 -0400

T7 RNAi Oligo Designer (TROD) aids in the design of DNA oligonucleotides for short interfering RNA (siRNA) synthesis with T7 RNA polymerase. It takes an input of a cDNA sequence and outputs a list of DNA oligos for ordering.

TFBScluster

Mon, 21 May 2012 03:50:04 -0400

TFBScluster is a web tool designed to identify clusters of transcription factor binding sites (TFBSs) conserved in mammalian and mouse genomes. By entering a specified range of TFBS, you can retrieve a list of SWISS-PROT characterized genes to which the clusters are localized.

Allen Brain Atlas

Mon, 18 Jul 2011 10:22:01 -0400

The Allen Brain Atlas (ABA) project has developed a web-based application designed to aid the intersection of neuroscience and genomics. The ABA Application enables users to access an extensive database of high resolution in situ hybridization (ISH) images from over 10,000 genes, reference atlases in both the sagittal and coronal planes, gene expression masks capturing the intensity of gene expression or signal, and the ability to search for gene expression by anatomic region.

Pseudomonas Genome Database

Mon, 14 May 2012 06:40:13 -0400

The Pseudomonas Genome Database integrates completely-sequenced Pseudomonas genome sequences and their annotations with genome-scale, high-precision computational predictions, experimental data, and manually curated, community-based annotation updates. Comparative genomics analyses incorporate robust genera-geared methods for predicting and clustering orthologs.

LitMiner

Sun, 20 May 2012 11:20:05 -0400

LitMiner is a literature data mining tool that is based on the annotation of key terms in article abstracts followed by statistical co-citation analysis of annotated key terms in order to predict relationships between genes, compounds, diseases and phenotypes, and tissues and organs.

PubMed Central

Sun, 20 May 2012 09:20:11 -0400

PubMed Central (PMC) is the U.S. National Institutes of Health (NIH) free digital archive of biomedical and life sciences journal literature.

SeqVISTA

Fri, 18 May 2012 07:40:12 -0400

Tool for sequence feature visualization and comparison; integrates with Internet Explorer; accepts GenBank Flat Files, GenBank HTML, FASTA files; plugins exist for visualization of output from RepeatMasker, PsiPred, and Cister.

RNApredator

Mon, 21 May 2012 01:00:08 -0400

RNApredator is a web server for the prediction of bacterial sRNA targets. The user can choose from a large selection of genomes. Accessibility of the target to the sRNA is considered.

MITOPRED

Sat, 19 May 2012 09:30:11 -0400

MITOPRED uses Pfam domains, pI values and amino acid composition to predict nuclear-encoded mitochondrial proteins. Predictions have been precomputed for a number of proteomes, as well as for all Eukaryotic sequences in Swiss-Prot and TrEMBL. Users may directly enter or upload a file with a list of protein sequences or Swiss-Prot/TrEMBL accession numbers.

SCLD

Sun, 20 May 2012 09:10:05 -0400

The Stem Cell Lineage Database (SCLD) user-editable lineage maps illustrating both endogenous development and the directed differentiation of human and mouse embryonic stem cells.

PhenomicDB

Sun, 20 May 2012 10:30:10 -0400

PhenomicDB integrates the genotype and phenotype information of several organisms from public data sources. The mapping of phenotypic data fields allows cross-species phenotype comparison.

PmiRKB

Sat, 19 May 2012 17:10:07 -0400

Plant miRNA knowledge base (PmiRKB) provides four major functional modules. In the 'SNP' module, single nucleotide polymorphism (SNP) data of seven Arabidopsis (Arabidopsis thaliana) accessions and 21 rice (Oryza sativa) subspecies were collected to inspect the SNPs within pre-miRNAs (precursor microRNAs) and miRNA-target RNA duplexes. A second module, 'Pri-miR', can be used to investigate the tissue-specific, transcriptional contexts of pre- and pri-miRNAs (primary microRNAs), based on massively parallel signature sequencing data. The third module, 'MiR-Tar', was designed to validate thousands of miRNA-target pairs by using parallel analysis of RNA end (PARE) data. The fourth module, 'Self-reg', also used PARE data to investigate the metabolism of miRNA precursors, including precursor processing and miRNA- or miRNA*-mediated self-regulation effects on their host precursors.

AgBase

Sun, 20 May 2012 13:20:12 -0400

AgBase provides resources to facilitate modeling of functional genomics data and structural and functional annotation of agriculturally important animal, plant, microbe and parasite genomes. One of seven new tools available at AgBase, GOModeler, supports hypothesis testing from functional genomics data. Moreover, we provide comprehensive training resources (including worked examples and tutorials) via links to Educational Resources at the AgBase website.

ERPIN

Wed, 16 May 2012 19:00:07 -0400

ERPIN (Easy RNA Profile IdentificatioN) takes as input an RNA sequence alignment and secondary structure annotation and will identify a wide variety of known RNA motifs (such as tRNAs, 5S rRNAs, SRP RNA, C/D box snoRNAs, hammerhead motifs, miRNAs and others) in your sequence(s) of interest. Also contains tool for drawing secondary structure of motifs.

PathGuide

Mon, 21 May 2012 04:20:05 -0400

The PathGuide - Pathway Resource List (PRL) is a database of 250+ links to resources for protein-protein interactions, metabolic and signalling pathways, transcription factor and genetic interaction networks, pathway diagrams, protein sequences, and protein-compound interactions.

chipD

Sun, 20 May 2012 19:00:10 -0400

chipD is a web server that facilitates the design of DNA oligonucleotide probes for high-density tiling arrays. The algorithm ensures probe specificity, thermodynamic properties amongst probe sets and target sequence coverage.

miRTarBase

Sun, 20 May 2012 13:50:04 -0400

miRTarBase database contains miRNA-target interactions (MTIs). The collected MTIs are validated experimentally by reporter assays, western blot, or microarray experiments with overexpression or knockdown of miRNAs.

ChimerDB

Sun, 20 May 2012 21:30:03 -0400

ChimerDB is a knowledgebase of fusion genes identified from bioinformatics analysis of transcript sequences in the GenBank and various other public resources such as the Sanger cancer genome project (CGP), OMIM, PubMed and the Mitelman's database. A new algorithm that is more sensitive, has detected 2699 fusion transcripts with high confidence. Furthermore, it can identify interchromosomal translocations as well as the intrachromosomal deletions or inversions of large DNA segments. Results from the analysis of next-generation sequencing data in the short read archives are incorporated along with a new alignment viewer.

3D-partner

Sat, 19 May 2012 18:50:08 -0400

3D-partner is a tool to predict interacting partners and binding models of a query protein sequence through the analysis of structural complexes.

CancerResource

Sat, 19 May 2012 09:30:04 -0400

CancerResource, a database that integrates cancer-relevant relationships of compounds and targets from (i) literature mining and (ii) external resources complemented with (iii) essential experimental and supporting information on genes and cellular effects. CancerResource addresses the spectrum of research on compound-target interactions in natural sciences as well as in individualized medicine.

NCBI Map Viewer

Sun, 20 May 2012 03:30:06 -0400

The NCBI Map Viewer provides graphical displays of features on NCBI\'s assembly of human genomic sequence data as well as cytogenetic, genetic, physical, and radiation hybrid maps.

Systems Biology Markup Language (SBML)

Mon, 21 May 2012 01:30:11 -0400

The Systems Biology Markup Language (SBML) is a computer-readable format for representing models of biochemical reaction networks. SBML is applicable to metabolic networks, cell-signaling pathways, genomic regulatory networks, and many other areas in systems biology.

deepBase

Mon, 21 May 2012 03:10:05 -0400

deepBase contains deep sequencing data from 185 small RNA libraries from diverse tissues and cell lines of seven organisms: human, mouse, chicken, Ciona intestinalis, Drosophila melanogaster, Caenhorhabditis elegans and Arabidopsis thaliana. deepBase facilitates the comprehensive annotation and discovery of small RNAs from transcriptomic data such as ncRNA-associated small RNAs (nasRNAs), promoter-associated small RNAs (pasRNAs), exon-associated small RNAs (easRNAs), repeat-associated small RNAs (rasRNAs) and miRNA and snoRNA candidates. For the purpose of comparative analysis, deepBase provides an integrative, interactive and versatile display.

Microbial Genome Viewer

Sat, 19 May 2012 00:50:14 -0400

Tool for visualization of microbial genomes. Chromosome wheels and linear genome maps with user specified features/color coding can be generated interactively. Graphics are created in SVG format.

EBI patent sequence database

Sat, 19 May 2012 07:50:05 -0400

The EBI Patent Sequence Database is a collection of non-redundant patent sequence databases, which cover the EMBL-Bank nucleotides patent class and the patent protein databases and contain value-added annotations from patent documents.

IGG

Thu, 17 May 2012 10:00:08 -0400

Integration of Genotypes from Genechips (IGG) is a Java-based tool with graphic interface to integrate genotypes across high throughput genotyping platforms from Affymetrix and Illumina and the HapMap Project. It is equipped with a series of functions to control qualities of genotype integration and to flexibly export genotypes for genetic studies as well.

Pathway Miner

Sat, 19 May 2012 19:10:04 -0400

Pathway Miner is a tool for searching lists of genes for associations in known pathway data from KEGG, BioCarta, and GenMAPP. Also provides statistical analyses.

WebGeSTer DB

Sun, 20 May 2012 22:20:07 -0400

WebGeSTer DB a database of intrinsic transcription terminators identified in bacterial genome sequences and plasmids. Users can obtain both graphic and tabular results on putative terminators based on default or user-defined parameters. The results are arranged in different tiers to facilitate retrieval, as per the specific requirements. An interactive map has been incorporated to visualize the distribution of terminators across the whole genome.

RepTar

Sun, 20 May 2012 23:10:11 -0400

RepTar is a database of miRNA target predictions, based on the RepTar algorithm that is independent of evolutionary conservation considerations and is not limited to seed pairing sites.

WormBase

Sun, 20 May 2012 03:40:04 -0400

Repository of mapping, sequencing and phenotypic information about C. elegans and C. briggsae.

pssRNAMiner

Sat, 19 May 2012 18:50:11 -0400

pssRNAMiner is a web server which identifies trans-acting siRNA clusters in plants, as well as their potential phase initiators. Users input a small RNA dataset and specify a transcript-genomic library for mapping.

MassTRIX

Sun, 20 May 2012 03:20:08 -0400

With applications in metabolomics and other mass spectrometry studies, MassTRIX is a hypothesis driven approach to the annotation of mass spectrometry data. Data is output in context on a KEGG pathway map.

RegPhos

Sat, 19 May 2012 15:20:18 -0400

RegPhos is a database for exploration of the phosphorylation network associated with an input of genes/proteins. Subcellular localization information is also included.

DBTSS

Sun, 20 May 2012 06:10:18 -0400

DataBase of Transcription Start Sites (DBTSS) is a database which contains precise positional information for transcription start sites (TSSs) of eukaryotic mRNAs. Included are 330 million new tags generated by massively sequencing the 5'-end of oligo-cap selected cDNAs in humans and mice. 31 different cell types or culture conditions are represented. Differential usage of alternative 5'-ends across cell types and conditions can be viewed in a series of new interfaces. Promoter sequence information is now displayed in a comparative genomics viewer where evolutionary turnover of the TSSs can be evaluated.

Full-parasites

Sat, 19 May 2012 21:50:10 -0400

Full-Parasites is a transcriptome database of apicomplexa parasites, which include Plasmodium and Toxoplasma species. It contains EST sequences, full length cDNAs, transcription start sites and RNA-seq data sets. Various types of cDNA data resources were interconnected with our original database functionalities. By providing the largest unique full-length cDNA and dynamic transcriptome data, Full-Parasites is useful for understanding host-parasite interactions.

Sol Genomics Network

Sun, 20 May 2012 17:10:09 -0400

The Sol Genomics Network (SGN) is a clade-oriented database (COD) containing biological data for species in the Solanaceae and their close relatives, with data types ranging from chromosomes and genes to phenotypes and accessions. SGN hosts several genome maps and sequences, including a pre-release of the tomato (Solanum lycopersicum cv Heinz 1706) reference genome. A new transcriptome component has been added to store RNA-seq and microarray data. The SGN curation model is community-driven, allowing researchers to add and edit information using simple web tools.

ScanProsite

Sun, 20 May 2012 00:50:11 -0400

ScanProsite is a tool for detecting PROSITE signature matches in protein sequences. Users can also search protein databases for specific motifs.

psRNATarget

Sun, 20 May 2012 19:10:09 -0400

psRNATarget is a plant small RNA target analysis server which features reverse complementary matching between small RNA and target transcript, and target site accessibility evaluation. It is designed for high-throughput analysis of next generation data, and outputs a comprehensive list of small RNA-target pairs.

ISfinder

Sun, 20 May 2012 21:50:06 -0400

ISfinder is a dedicated insertion sequence (IS) database which assigns names to individual ISs to maintain a coherent nomenclature, an IS repository including >3000 individual ISs from both bacteria and archaea and provides a basis for IS classification. Each IS is indexed in ISfinder with various associated pieces of information (the complete nucleotide sequence, the sequence of the ends and target sites, potential open reading frames, strain of origin, distribution in other strains and available bibliography) and classified into a group or family to provide some insight into its phylogeny. ISfinder also includes extensive background information on ISs and transposons in general. ISbrowser, an extension to the ISfinder platform and a tool, which permits visualization of the position, orientation and distribution of complete and partial ISs in individual prokaryotic genomes.

NCBI Taxonomy Database

Thu, 17 May 2012 16:50:15 -0400

Taxonomic classification of all organisms with sequences in GenBank.

BSQA

Tue, 15 May 2012 15:30:03 -0400

BeeSpace Question/Answering (BSQA) system is a web server that performs integrated text mining for insect biology, covering diverse aspects from molecular interactions of genes to insect behavior. BSQA recognizes a number of entities and relations in Medline documents about the model insect, Drosophila melanogaster.

DCODE.ORG

Mon, 21 May 2012 00:40:11 -0400

The dcode.org website provides access to tools for comparative genomic analyses developed by the Comparative Genomics Center at the Lawerence Livermore National Laboratory. Tools include: zPicture, Mulan, eShadow, rVista, CREME, and the ECR Browser.

Prospectr

Thu, 17 May 2012 23:50:19 -0400

Prospectr (PRiOrization by Sequence & Phylogenetic Extent of CandidaTe Regions) can be used to enrich lists of genes found at a suspected disease locus. Given a list of genes, Prospectr will return a ranked list ordered by the likelihood of involvement in disease.

SerbGO

Sat, 19 May 2012 14:10:04 -0400

Searching for the best GO tool (SerbGO) helps users select the GO annotation or list analysis tools which best suit their needs. SerbGO may also be used to compare the capabilities of the various GO tools in the context of the users' experiment.

metaSHARK

Thu, 17 May 2012 11:30:12 -0400

Metabolic Search And Reconstruction Kit (metaSHARK) provides an interactive visualisation platform for the KEGG metabolic network in the form of the SHARKview applet.

UCSC Cancer Genomics Browser

Fri, 18 May 2012 15:20:07 -0400

The UCSC Cancer Genomics Browser comprises a suite of web-based tools to integrate, visualize and analyze cancer genomics and clinical data. The browser displays whole-genome views of genome-wide experimental measurements for multiple samples alongside their associated clinical information. Multiple data sets can be viewed simultaneously as coordinated 'heatmap tracks' to compare across studies or different data modalities. Users can order, filter, aggregate, classify and display data interactively based on any given feature set including clinical features, annotated biological pathways and user-contributed collections of genes. Integrated standard statistical tools provide dynamic quantitative analysis within all available data sets. Many new features have been added, including the hgMicroscope tumor image viewer, hgSignature for real-time genomic signature evaluation on any browser track, and 'PARADIGM' pathway tracks to display integrative pathway activities.

MirZ

Tue, 15 May 2012 20:10:07 -0400

MirZ is a web server that for evaluation and analysis of miRNA. It integrates two miRNA resources: the smiRNAdb miRNA expression atlas and the E1MMo miRNA target prediction algorithm.

SNPsyn

Mon, 21 May 2012 00:30:10 -0400

SNPsyn is a tool for the discovery of synergistic pairs of SNPs from large genome-wide case-control association studies data on complex diseases. The SNPsyn web server receives GWAS data submissions, invokes the interaction analysis and returns results. The user can explore details on identified SNP-SNP pairs, perform gene set enrichment analysis and interact with the constructed SNP synergy network.

SNPinfo

Sat, 19 May 2012 01:00:09 -0400

A suite of web=based tools for SNP detection. Functional predictions of SNP affect on protein structure, gene regulation, splicing and miRNA binding are incorporated.

ACID

Fri, 18 May 2012 17:50:13 -0400

The Array Clone Information Database (ACID) is a searchable resource for information about human, mouse, and rat cDNA clones. Each clone contains information about the assigned UniGene cluster(s), location in the full-length transcript, assigned gene ontology terms and position in the genome assembly.

GeSBAP

Sat, 19 May 2012 13:40:06 -0400

Gene Set based Analysis of Polymorphisms (GeSBAP) implements the gene set analysis to the evaluation of genome wide association studies. Gene set analysis is based on testing the association of modules of functionally related genes.

TIGR Software Tools

Sat, 19 May 2012 18:30:09 -0400

A list of open-source software packages available for free from The Institute for Genomic Research (TIGR).

RegRNA

Sat, 19 May 2012 10:30:13 -0400

Regulatory RNA (RegRNA) is a server for identifying regulatory RNA motifs and elements in mRNA sequences including: motifs located in the 5\'-UTR and 3\'-UTR; motifs involved in mRNA splicing and transcriptional regulation; other motifs in mRNA such as riboswitches and splice donor/acceptor sites; RNA structural features; and miRNA target sites.

AntiHunter 2.0

Tue, 15 May 2012 21:20:04 -0400

AnitHunter 2.0 is a tool to detect potential EST antisense transcripts within a given genomic region from the analysis of BLAST output.

PatMatch

Sat, 19 May 2012 03:40:19 -0400

PatMatch is a pattern matching tool that allows you to search for short (<20 residues) nucleotide or peptide sequences and can accomodate ambiguous/degenerate patterns.

TOUCAN 2

Sun, 20 May 2012 22:40:15 -0400

TOUCAN 2 is a regulatory sequence analysis workbench for Metazoan sequences, directly linked with the Ensembl database and implementing SOAP clients for diverse alignment and motif detection algorithms.

CONREAL

Thu, 17 May 2012 00:10:27 -0400

CONREAL (Conserved Regulatory Elements Anchored Alignment) allows identification of transcription factor binding sites (TFBS) that are conserved between two orthologous promoter sequences.

PAZAR

Sun, 03 Oct 2010 00:45:42 -0400

PAZAR is an open access and open source database of transcription factor and regulatory sequence annotation with associated web interface and programming tools designed to submit and query data related to the regulation of gene expression.

TraFaC

Sun, 20 May 2012 10:10:11 -0400

TraFaC (Transcription Factor Binding Site Comparison) is a tool that identifes regulatory regions using a comparative sequence analysis approach.

Gibbs Motif Sampler

Sun, 20 May 2012 19:10:06 -0400

Gibbs Motif Sampler allows you to identify motifs, conserved regions, in DNA or protein sequences. This tool can be applied for the detection of transcription factor binding sites (TFBS).

GoSurfer

Mon, 18 Jul 2011 14:13:36 -0400

GoSurfer is a tool for visualizing and comparing gene sets by mapping them onto Gene Ontology (GO) information in the form of a hierarchical tree. It is useful for investigating the results of microarray analyses or genome-wide computations.

ReadOut

Mon, 21 May 2012 01:20:09 -0400

Readout is a server for the calculation of direct and indirect readout energy Z-scores which estimate the degree of sequence specificity of the protein-DNA complex. Readout can be useful for checking the quality of protein-DNA interactions in three dimensional (3D) structures.

RSAT

Mon, 21 May 2012 03:20:03 -0400

Regulatory Sequence Analysis Tools (RSAT) detects regulatory signals in non-coding sequences; tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Tools may be accessed separately or connected to other tools. As well, the tools are available as web services for integration into programmatic work flows. New tools incorporated include an automated sequence retrieval from EnsEMBL, motif comparison and motif quality tools, and the capacity to process ChIP-sequence data.

WebMOTIFS

Wed, 16 May 2012 14:40:09 -0400

WebMOTIFS is a tool for motif discovery, scoring, analysis, and visualization. It allows you to use different programs (AlignACE, MDscan, MEME, and Weeder) to search for DNA-sequence motifs, and evaluate the results.

MatchMiner

Mon, 21 May 2012 02:40:10 -0400

MatchMiner is a tool to compare and convert gene identifiers. Users can translate single or lists of identifiers from one form to another, or compare two lists of identifiers for common gene references.

Riboswitch finder

Sun, 20 May 2012 19:20:09 -0400

RNA motif search program that identifies RNA motifs called riboswitches which are metabolic binding domains in mRNA that regulate gene expression. The program was originally designed around a set of riboswitches found in Bacillus subtilis.

DEQOR

Sun, 20 May 2012 01:10:10 -0400

Tool which aids in the design and quality control of small interfering RNAs (siRNAs) for RNA interference (RNAi) and gene silencing. It evaluates the inhibitory potency of potential siRNA sequences as well as identifying gene regions that have a high silencing capacity.

G-SESAME

Sat, 19 May 2012 01:20:09 -0400

G-SESAME is a suite of online tools for measuring the semantic similarities of Gene Ontology (GO) terms and the functional similarities of gene products, as well as data mining the GO database.

OrthoSelect

Sun, 20 May 2012 12:00:07 -0400

OrthoSelect web server detects orthologous gene sequences in EST libraries and outputs orthologous gene alignments. Annotations, data matrices for each gene, and the gene alignments may also be visualized.

GenePath2

Fri, 18 May 2012 14:40:27 -0400

GenePath is a tool for automated construction of genetic networks and proposal of genetic experiments from mutant data.

CAPweb

Sun, 20 May 2012 20:00:05 -0400

CGH array Analysis Platform (CAPweb) is a tool for storing, analyzing and visualizing CGH-array data.

NXSensor

Sun, 20 May 2012 23:10:08 -0400

Nucleosome eXclusion Sensor (NXSensor) finds potential nucleosome-free regions of DNA sequences. NXSensor can be used to assess the likelihood of nucleosome formation in regions involved in gene regulation and other aspects of chromatin function.

E-RNAi

Sun, 20 May 2012 11:30:05 -0400

E-RNAi is a tool for designing and evaluating dsRNA constructs suitable for RNAi experiments in 12 organisms including Drosophila, C. elegans, human and other emerging model organisms. E-RNAi also facilitates the design of secondary RNAi reagents for validation experiments, evaluation of pooled siRNA reagents and batch design.

BROP

Sat, 19 May 2012 09:50:17 -0400

The Bioinformatics Resource for Oral Pathogens (BROP) contains tools for genomics of oral pathogens including Genome Viewer, GOAL (genome wide ORF alignment), an oral pathogen microarray database, an entrez counter, oral pathogen specific BLAST, and a codon usage database.

MEME Suite

Fri, 18 May 2012 16:40:08 -0400

The MEME Suite web server is a unified portal for discovery and analysis of sequence motifs (e.g. DNA binding sites, protein interaction domains). Motifs with/without gaps may be discovered, searched for in DNA and protein databases, compared to other motifs and analyzed for putative function by association with gene ontology terms. MEME is a tool designed for discovering and searching for DNA motifs such as transcription factor binding sites (TFBS) or protein domains.

Gendoo

Sat, 19 May 2012 06:10:08 -0400

Gene Disease Features Ontology-based Overview System (Gendoo) is a web tool for visualizing disease feature profiles generated from the assignment of MeSH vocabulary for associated drugs, biological phenomena and anatomy to OMIM data. This approach assists in interpreting -omic data for its molecular and clinical aspects.

REDfly

Sun, 20 May 2012 21:30:11 -0400

Regulatory Element Database for Drosophila (REDfly) is a curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs). REDfly seeks to include all experimentally verified fly CRMs along with their DNA sequence, their associated genes, and the expression patterns they direct.

GSA-SNP

Mon, 21 May 2012 04:10:08 -0400

GSA-SNP web server performs gene set analysis (GSA) on genome-wide association data, using 3 different GSA methods.

PINT

Sun, 20 May 2012 23:30:04 -0400

Pathway INtegration Tool (PINT) allows integration and annotation of systems biology markup language (SBML) files from a variety of sources. Gene list files are also accepted.

IDconverter

Sun, 03 Oct 2010 00:44:28 -0400

IDconverter is a tool that converts gene, clone or protein IDs to other IDs which can be especially useful for microarray data analyses. This application is part of the suite Asterias.

miRU

Sat, 19 May 2012 11:10:05 -0400

miRU is a tool that takes as an input a small miRNA sequence and then searches for complementary matches in TIGR plant-specific gene data sets to predict potential target genes.

DRTF

Sun, 20 May 2012 11:00:13 -0400

Database of Rice Transcription Factor (DRTF) is a collection of known and predicted transcription factors from japonica and indica rice genomes.

STAMP

Thu, 17 May 2012 22:50:22 -0400

STAMP is a tool for exploring DNA-binding motif similarities by providing resources for motif alignment, similarity and database matching.

DATF

Fri, 18 May 2012 05:30:05 -0400

The Database of Arabidopsis Transcription Factors (DATF) contains information of more than 1800 known and predicted transcription factors for Arabidopsis.

RNAhybrid

Sun, 20 May 2012 14:50:07 -0400

RNAhybrid is a tool for predicting miRNA (microRNA) targets by calculating the minimum free energy of hybridization between target RNA and miRNA sequences.

siVirus

Mon, 21 May 2012 02:50:06 -0400

siVirus aids in the design of short interfering RNA (siRNA) and helps to identify conserved target sequences for antiviral RNA interference.

MelinaII

Sun, 20 May 2012 14:40:12 -0400

MelinaII (Motif Elucidator in Nucleotide Sequence Assembly) can run multiple motif prediction tools (Consensus, MEME, Gibbs Sampler, MDScan, Weeder) simultaneously. Graphical results can be used to compare predictions of potential DNA motifs (such as transcription factor binding sites, TFBS) in promoter regions.

Sfold

Sat, 19 May 2012 09:30:08 -0400

Server with three tools for the rational design of small interfering RNAs (Sirna), antisense oligonucleotides (Soligo), and trans-cleaving ribozymes (Sribo). A fourth tool, Srna, returns output including general folding features.

PRI-CAT

Fri, 18 May 2012 00:20:04 -0400

PRI-CAT is a web-based workflow tool for the management and analysis of plant ChIP-seq experiments, with focus on Arabidopsis. Secondary analysis can be performed with the aid of GALAXY.

Chinook

Tue, 15 May 2012 02:30:04 -0400

Chinook is a peer-to-peer (P2P) service for the discovery, use and assessment of bioinformatics programs. Chinook Online allows researchers to connect and run distributed bioinformatics programs using a web application.

SIREs

Sat, 19 May 2012 21:50:05 -0400

SIREs is an iron responsive element prediction tool. From input data, SIREs produces structure analysis, predicted RNA folds, folding energy data and overall quality flags.

BioBayesNet

Sun, 20 May 2012 05:20:10 -0400

BioBayesNet is a server for feature extraction and Bayesian network modeling of biological sequence data.

PlantTFDB

Sun, 03 Oct 2010 00:45:42 -0400

Genome Surveyor

Sun, 20 May 2012 20:30:11 -0400

Genome Surveyor is a tool for discovery and analysis of cis-regulatory elements and transcription factors in Drosphila built on the GBrowse genome browser.

cisRED

Sat, 19 May 2012 06:40:09 -0400

cisRED is a database system for genome-scale computational discovery of regulatory elements.

PromoterWise

Sun, 03 Oct 2010 00:43:23 -0400

Compares two DNA sequences allowing for inversions and translocations, ideal for promoters.

SITECON

Tue, 15 May 2012 13:30:10 -0400

Server for the detection of conformational and physicochemical properties in transcription factor binding sites and potential binding sites.

VOMBAT

Thu, 17 May 2012 21:30:08 -0400

VOMBAT predicts transcription factor binding sites (TFBS) and other motifs in sequence data based on Variable Order Markov models and variable order BAyesian Trees.

SSA

Thu, 17 May 2012 15:40:18 -0400

Signal Search Analysis (SSA) allows for the analysis of nucleic acid sequence motifs that are positionally correlated with a functional site (e.g. a transcription start site).

SiteSeer

Sun, 20 May 2012 13:00:10 -0400

SiteSeer is a visualization tool for mapping transcription factor binding sites (TFBS) in the upstream regions of single or grouped eukaryotic genes.

FirstEF

Fri, 18 May 2012 11:10:05 -0400

First Exon Finder (FirstEF) is a 5\' terminal exon and promoter prediction program. It consists of different discriminant functions structured as a decision tree.

iCR

Sun, 20 May 2012 19:00:08 -0400

Identify Conserved targets of a Regulon (iCR) predicts regulatory binding sites based on conservation across multiple species. The user provides an ungapped multiple sequence alignment representing the regulatory binding site. iCR reports back with predicted binding sites that are conserved and highlights the downstream co-regulated genes.

ZiFiT

Fri, 18 May 2012 14:30:14 -0400

ZiFiT (Zinc Finger Targeter) assists in the design of zinc finger proteins that can bind to specific DNA sequences. ZiFiT has been updated to integrate additional tools and resources including scoring schemes for modular assembly, an interface with the Zinc Finger Database of engineered ZFPs, and direct query of NCBI BLAST servers for identification of potential off-target sites within a host genome.

RegPredict

Sun, 20 May 2012 23:20:09 -0400

RegPredict web server provides comparative genomics tools for reconstruction and analysis of microbial regulons using comparative genomics.

rMotif

Sat, 19 May 2012 09:30:12 -0400

rMotif provides tools for the discovery of de-novo, fully, or partially characterized regulatory motifs including transcription factor binding sites (TFBS).

rVISTA

Sat, 19 May 2012 05:30:07 -0400

Server which detects transcription factor binding sites(TFBS) through combining TFBS prediction, sequence comparison and cluster analysis.

Consite

Sun, 20 May 2012 18:40:05 -0400

Detect transcription factor binding sites in genomic sequences using phylogenetic footprinting and experimentally-confirmed binding profiles.

MicroFootPrinter

Sat, 19 May 2012 23:10:07 -0400

MicroFootPrinter identifies the conserved motifs in regulatory regions of prokaryotic genomes using the phylogenetic footprinting program FootPrinter.

Match

Fri, 18 May 2012 19:50:05 -0400

Match is a weight matrix-based tool which searches for putative transcription factor binding sites (TFBS) in DNA sequences. Registration at the site is free and is required to use Match.

Eponine

Sat, 19 May 2012 23:10:05 -0400

Eponine is a probabilistic method for detecting transcription start sites (TSS) in mammalian genomic sequence, with good specificity and excellent positional accuracy.

siDirect

Sat, 19 May 2012 11:50:05 -0400

Server for computing small interfering RNA (siRNA) sequences which are best suited for mammalian RNA interference (RNAi). The site accepts a sequence as input and returns a list of siRNA candidates.

Cluster Buster

Sun, 20 May 2012 07:40:11 -0400

Cluster Buster is a tool that finds clusters of pre-specified motifs in DNA sequences.

PredictRegulon

Sat, 19 May 2012 22:30:09 -0400

PredictRegulon is a tool that, for a given regulatory protein and prokaryotic genome, predicts binding sites and operons. The user selects a prokaryote genome and provides an ungapped multiple sequence alignment representing the binding site. PredictRegulon reports back with predicted binding sites and downstream co-regulated genes.

ConTra

Mon, 21 May 2012 00:50:06 -0400

The Conserved Transcription Factor Binding Sites (ConTra) is a promoter alignment analysis tool to identify transcription factor binding sites across species. This web server allows users to interactively visualize transcription factor binding sites predicted using TransFac, JASPAR or PWM libraries on aligned promoter sequences. Nine reference organisms are supported for analysis of promoter regions, 5' UTRs, 3' UTRs and introns.

MicroInspector

Thu, 17 May 2012 15:40:05 -0400

MicroInspector is a tool that detects miRNA (microRNA) binding sites in your input sequence by searching against databases of known miRNA binding sites.

Drosophila DNase I footprint database

Sun, 20 May 2012 21:10:06 -0400

Database of transcription factor binding sites created from systematic literature curation and genome annotation of DNase I footprints for Drosophila.

CSTminer

Mon, 21 May 2012 04:00:07 -0400

CSTminer searches for Conserved Sequence Tags (CST) in pairwise comparisons of genomic sequences. Output is a graphical map showing the location of CSTs overlayed with known Ensembl exons and ESTs. A scoring system reflects coding or non-coding potential of these conserved blocks.

PROSITE

Sat, 19 May 2012 06:10:04 -0400

Database of protein families and domains defined from SwissProt database; consider also checking specific motif databases such as PhosphoBase.

siRNAdb

Sun, 03 Oct 2010 00:45:41 -0400

This resource includes siSearch, AOSearch, and a siRNAdb which provides a platform for mining an siRNA database, and searching for non-specific matches to your siRNA (small interfering RNAs).

siRNA Selection Server

Sat, 19 May 2012 01:10:06 -0400

Server aiding the design of short interfering RNAs (siRNAs) by providing information on stability, SNPs and specificity of a potential siRNA.

CENTDIST

Sat, 19 May 2012 12:30:06 -0400

CENTDIST is a co-motif scanning program to identify co-transcription factors. CENTDIST ranks co-transcription factors based on their distribution around CHIP-seq peaks.

MADAP

Sat, 19 May 2012 01:20:05 -0400

MADAP is a clustering tool for the interpretation annotation data mapped onto complete or partial genome sequences. Initially developed for determining transcription start sites (TSS) by defining 5\' and 3\'ends of mRNA, MADAP also has utility in clustering other annotation data types (ChIP-chip data, for example).

PromH

Mon, 21 May 2012 01:00:06 -0400

PromH predicts transcription start sites (TSS), TATA boxes, and transcription factor binding sites (TFBS) in promoter regions using pairs of orthologous sequences.

jPREdictor

Thu, 17 May 2012 18:50:04 -0400

jPREdictor predicts cis-regulatory elements using short motifs that are known to bind regulatory proteins. Predictions are made by searching for clusters of these motifs, and weighting these clusters by applying a positive or negative training sets to score the sequence.

dsCheck

Sat, 19 May 2012 01:30:08 -0400

dsCheck takes a nucleotide sequence as input and estimates off-target effects caused by dsRNA (double-stranded RNA) employed in RNAi studies. dsCheck can be used either to verify previously designed dsRNA sequences, or to design off-target minimized dsRNAs.

miRanalyzer

Sun, 20 May 2012 09:20:12 -0400

miRanalyzer is a web server tool for the analysis of high throughput sequencing experiments for microRNAs. Users input a list of unique reads and copy number. The tool detects all known microRNA sequences annotated in miRBase, finds perfect matches in other libraries of transcribed sequences and predicts new microRNAs. Alignments are based on Bowtie and differences between plant and animal microRNAs are accounted for in prediction.

JASPAR

Sat, 19 May 2012 20:10:05 -0400

JASPAR is a non-redundant, curated collection of transcription factor binding profiles. Each profile is generated from published, experimentally defined eukaryotic transcription factor binding sites.

WebTraceMiner

Sun, 20 May 2012 07:50:25 -0400

WebTraceMiner is a tool for processing and mining Expressed Sequence Tag (EST) trace files. It can help characterize 3\' and 5\' termini of cDNA inserts by detecting sequence features such as vector fragments, adapter/linker sequences, insert-flanking restriction endonuclease recognition sites, and polyA or polyT tails.

Pathway Hunter Tool

Tue, 15 May 2012 01:20:05 -0400

Pathway Hunter Tool (PHT) uses shortest path analysis to reconstruct and visualize biochemical pathways. The user can find the shortest path between two metabolites, or find all reachable products or educts for a given metabolite.

ASmodeler

Sat, 19 May 2012 17:30:16 -0400

Gene modeling server which focuses on the modeling of alternative splicing. It is based on the alignment of mRNA, EST and protein sequences and combines genome-based clustering and transcript assembly. Supports human, mouse and rat genomes.

Alternative Splicing Gallery

Mon, 21 May 2012 05:20:08 -0400

The Alternative Splicing Gallery (ASG) takes an identifier such as an EnsEMBL gene ID or a RefSeq ID as input, and provides a graph mapping splice events to transcript information. The user can also view GO information for the record, and select one or more exons and download the resulting sequence. ASG also links out to other alternative splicing databases like ProSplicer.

QGRS Mapper

Mon, 21 May 2012 04:40:07 -0400

Quadruplex forming G-Rich Sequences (QGRS) Mapper searches nucleotide sequences for the presence of G-quartet motifs. QGRS Mapper allows you to view the distribution and composition of QGRS in the context of alternatively spliced isoforms of your gene.

AStalavista

Wed, 16 May 2012 16:30:12 -0400

AStalavista (alternative splicing transcriptional landscape visualization tool) dynamically identifies, extracts, and displays alternative splicing events from whole genome annotations and user provided gene sets.

CaSNP

Sun, 20 May 2012 02:00:07 -0400

CaSNP database for storing and interrogating quantitative copy number alterations (CNA) data from SNP arrays on 34 different cancer types in 104 studies. With a user input of region or gene of interest, CaSNP will return the CNA information summarizing the frequencies of gain/loss and averaged copy number for each study, and provide links to download the data or visualize it in UCSC Genome Browser. CaSNP also displays the heatmap showing copy numbers estimated at each SNP marker around the query region across all studies for a more comprehensive visualization.

NAST

Sat, 19 May 2012 07:40:17 -0400

Nearest Alignment Space Termination (NAST) is a multiple sequence alignment server for comparative analysis of 16S rRNA gene sequences from bacteria and archaea.

AmoebaDB and MicrosporidiaDB

Sun, 20 May 2012 11:40:08 -0400

AmoebaDB and MicrosporidiaDB are functional genomic databases serving the amoebozoa and microsporidia research communities, respectively. AmoebaDB contains the genomes of three Entamoeba species (E. dispar, E. invadens and E. histolityca) and microarray expression data for E. histolytica. MicrosporidiaDB contains the genomes of Encephalitozoon cuniculi, E. intestinalis and E. bieneusi. Genomic scale data can be queried based on BLAST searches, annotation keywords and gene ID searches, GO terms, sequence motifs, protein characteristics, phylogenetic relationships and functional data such as transcript (microarray and EST evidence) and protein expression data. Search strategies can be saved within a user's profile for future retrieval and may also be shared with other researchers using a unique strategy web address.

FlyBase

Thu, 17 May 2012 17:40:15 -0400

FlyBase is a database of genetic and molecular data for Drosophila. FlyBase includes data on all species from the family Drosophilidae; the primary species represented is Drosophila melanogaster.

Servers at University College London

Sun, 20 May 2012 17:20:06 -0400

A suite of tools that includes: PSIPRED, a protein structure prediction server; GenTHREADER, for genomic protein fold recognition; MEMSAT2, for transmembrane protein structure prediction; GTD, the genomic threading database; DISOPRED, a dynamic disorder prediction server; DomPred, a domain prediction server; and COPS, for the comparison of protein structure classifications. UCL web portal has been updated to include a fully automated 3-D modeling pipeline, BioSerf.

PREP Suite

Sun, 20 May 2012 12:40:04 -0400

The PREP (Predictive RNA Editors for Plants) suite predicts sites of RNA editing based on the principle that editing in plant organelles increases the conservation of proteins across species. Predictors for mitochondrial genes, chloroplast genes, and alignments input by the user are included.

Recode

Sat, 19 May 2012 19:30:05 -0400

Recode2 is a database of genes that utilize non-standard translation for gene expression purposes. Recoding events described in the database include programmed ribosomal frameshifting, translational bypassing (aka hopping) and mRNA specific codon redefinition. Recode-2 provides access to detailed information on genes known to utilize translational recoding and allows complex search queries, browsing of recoding data and enhanced visualization of annotated sequence elements.

Geno2pheno

Sat, 12 May 2012 06:40:06 -0400

Geno2pheno takes as input an HIV-1 pol-gene DNA sequence and estimates phenotypic drug resistance to 17 antiretroviral drugs.

MobilomeFINDER

Mon, 21 May 2012 01:20:11 -0400

MobilomeFINDER (Mobile Genome FINDER) is a tool for high-throughput genomic island discovery.

PlantTFDB 2.0

Fri, 18 May 2012 19:50:06 -0400

The PlantTFDB 2.0 plant transcription factor (TF) database contains detailed annotation including general information, domain feature, gene ontology, expression pattern and ortholog groups, as well as cross references to various databases and literature citations for these TFs. Multiple sequence alignments and phylogenetic trees for each family can be shown as Weblogo pictures or downloaded as text files.

MetaPath Online

Wed, 16 May 2012 19:30:07 -0400

MetaPath Online gives users access to an algorithm for network expansion. Starting with given metabolites, called seed compounds, the algorithm uses known information about metabolic reactions and pathways to expand the network and define scope. This systematic investigation of structure-function relationships of metabolic networks can offer evolutionary insights.

DISULFIND

Fri, 18 May 2012 19:20:10 -0400

DISULFIND is a server for predicting the disulfide bonding state of cysteines and their disulfide connectivity given a protein sequence.

TmPrime

Sun, 20 May 2012 21:40:08 -0400

TmPrime allows users to design oligonucleotide sets for gene assembly by both ligase chain reaction and polymerase chain reaction. The program also provides functions to separate long genes into smaller fragments for multi-pool assembly and codon optimization for expression.

SEPACS

Sun, 20 May 2012 10:40:05 -0400

SEPACS (Seroreactivity Pattern Classification System) is a a web-based application for classification of seroreactivity profiles.

Ensembl Genome Browser

Sun, 20 May 2012 21:20:09 -0400

Website, MySQL server and perl API access to software system which produces and maintains automatic annotation on eukaryotic genomes.

Berkeley Phylogenomics Group

Sun, 20 May 2012 16:40:06 -0400

The Berkeley Phylogenomics Group provides a series of web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction, and SCI-PHY subfamily identification.

PipeAlign

Sat, 19 May 2012 19:00:09 -0400

PipeAlign takes one or more protein sequences as input and analyzes them in a five-step process during which searches for sequence homologues, analyses of multiple sequence alignments, and hierarchical relationships between protein subfamilies are performed.

VISTA

Mon, 21 May 2012 02:40:08 -0400

VISTA is a comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species.

CLIPZ

Fri, 18 May 2012 19:20:05 -0400

CLIPZ supports the automatic functional annotation of short reads resulting primarily from crosslinking and immunoprecipitation experiments (CLIP) performed with RNA-binding proteins in order to identify the binding sites of these proteins. The functional annotation could be also applied to short reads resulting from other type of experiments such as mRNA-Seq, Digital Gene Expression, small RNA cloning, etc. The CLIPZ platform enables visualization and mining of individual data sets as well as analysis involving multiple experimental data sets.