Bioinformatics Links Directory - NAR Web Server Issue 2005

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.

ARGO

Mon, 14 May 2012 22:40:08 -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.

ArrayXPath

Thu, 10 May 2012 22:30:10 -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.

ARTS

Wed, 16 May 2012 13:10:06 -0400

ARTS (Advanced Retrieval Tool for SNPs) can be used to retrieve SNP that are polymorphic between several different mouse strains to aid in the design of genome-wide SNP marker panels.

ASePCR

Wed, 16 May 2012 16:00:20 -0400

ASePCR (Alternative Splicing electronic PCR) is a tool for carrying out e-PCR to detect differences in amplicon sizes in transcripts from different tissues and organs.

Assembly PCR Oligo Maker

Wed, 16 May 2012 19:30:09 -0400

Assembly PCR Oligo Maker is a tool for designing oligodeoxynucleotides for the PCR based construction of long DNA molecules.

AthaMap

Wed, 16 May 2012 06:50:06 -0400

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

AUGUSTUS

Tue, 15 May 2012 01:30:08 -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.

AutoSNPdb

Wed, 16 May 2012 17:50:05 -0400

SNPServer combines BLAST, cap3 and a SNP discovery module into a single pipeline for the discovery of SNPs in user submitted files or dynamically created assemblies.

Babelomics

Wed, 16 May 2012 07:00:05 -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.

BASys

Sun, 13 May 2012 01:40:14 -0400

BASys (Bacterial Annotation System) is a tool for automated annotation of bacterial genomic (chromosomal and plasmid) sequences including gene/protein names, GO functions, COG functions, possible paralogues and orthologues, molecular weights, isoelectric points, operon structures, subcellular localization, signal peptides, transmembrane regions, secondary structures, 3-D structures, reactions, and pathways.

BhairPred

Tue, 15 May 2012 21:20:06 -0400

BhairPred is a tool for predicting beta-hairpins in protein sequences using a support vector machine.

Bioinformatics Links Directory

Mon, 07 May 2012 01:10:05 -0400

The Bioinformatics Links Directory features curated links to molecular resources, tools and databases. All of the resources are free or available for a nominal fee.

Bioverse

Tue, 15 May 2012 16:40:08 -0400

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

BROP

Tue, 15 May 2012 21:10:40 -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.

CAMPO

Mon, 14 May 2012 05:40:12 -0400

CAMPO is a tool to analyze conserved regions from a multiple sequence alignment

CBS DAS protein viewer

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

The CBS DAS protein viewer uses the distributed annotation system (DAS) to integrate and present annotation data from multiple sources for a protein sequence.

CCT

Tue, 15 May 2012 19:00:09 -0400

CCT (Current Comparative Table) is a software package that you can install and set-up on your own system to help you to maintain and search databases.

CHAOS/DIALIGN WWW server

Tue, 15 May 2012 20:00:04 -0400

The CHAOS/DIALIGN WWW server is a multiple sequence alignment site which passes input sequences through CHAOS to create a list of local similarites. These similarities serve as anchor points, allowing DIALIGN to conduct global alignments faster. ABC can then be used for the interactive visualization of the alignment.

CHC_FIND

Thu, 17 May 2012 02:30:06 -0400

CHC_FIND is a tool to analyze conserved hydrophobic contacts (CHC) from multiple structural alignments. In addition to a multiple sequence alignment, a structural alignment which provides the superposition of structurally conserved regions (SCRs) (i.e., results from SCR_FIND) needs to be provided.

CisMols

Thu, 17 May 2012 02:40:18 -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.

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.

ConSurf

Mon, 07 May 2012 16:30:04 -0400

The ConSurf server allows one to map levels of amino acid conservation to known protein structures in order to study areas of potential functional importance on the surface of the protein. A PDB file is required as input, and a multiple sequence alignment is optional. If an alignment is not provided, ConSurf will build one by performing a search for homologous sequences and then aligning them. ConSurf 2010 combines ConSurf and ConSeq for an easier, more intuitive interface.

DCODE.ORG

Sun, 13 May 2012 22:20:05 -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.

DeNovoID

Mon, 14 May 2012 21:40:10 -0400

DeNovoID is a tool for protein identification using de novo peptide sequence data from mass spectrometry experiments.

DIAL

Sun, 13 May 2012 17:50:08 -0400

DIAL (Domain Identification Algorithm) is a web server for the automatic identification of structural domains given the three-dimensional coordinates of a protein.

DiANNA

Wed, 16 May 2012 09:50:07 -0400

DiANNA (DiAminoacid Neural Network Application) a tool that predicts cysteine states of a protein. It can predict whether a particular cysteine is reduced, is forming a disulfide bond, or is bound to a metallic ligand.

DINAMelt

Fri, 11 May 2012 08:20:09 -0400

DINAMelt is a tool for predicting hybridization and folding (secondary structure) of DNA and RNA using equilibrium thermodynamic methods.

dsCheck

Thu, 17 May 2012 00:40:20 -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.

E-RNAi

Sat, 12 May 2012 09:50:04 -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.

EBI Tools

Mon, 14 May 2012 21:30:05 -0400

EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies.

enoLOGOS

Wed, 16 May 2012 22:10:07 -0400

enoLOGOS creates sequence logos based on a variety of input, including sequence alignments, probability and alignment matrices and energy measurements.

EVAcon

Wed, 16 May 2012 01:10:05 -0400

EVAcon automates the continuous evaluation of inter-residue contact prediction servers. Results can be viewed statically or dynamically generated.

Expression Profiler

Wed, 16 May 2012 19:40:06 -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.

FeatureExtract

Sun, 13 May 2012 14:00:05 -0400

The FeatureExtract server extracts sequence and feature annotations, such as intron/exon structure, from GenBank entries and other GenBank format files.

FF - Fragment Finder

Sun, 13 May 2012 15:20:07 -0400

FF (Fragment Finder) takes a PDB ID, a structure coordinate file or a list of phi and psi angles as input and searches for matches to a specified structural fragment. Users can tailor the search based on sequence similarity and vary the dataset searched against.

FFAS

Tue, 15 May 2012 08:10:11 -0400

The Fold & Function Assignment System (FFAS) takes an amino-acid sequence as input and generates a profile which is compared to several sets of sequence profiles including PDB, SCOP, and PFAM. Public metagenomic sequence data has been added to FFAS, so that the profile of a user's protein can be compared to 20 additional profile databases including several complete proteomes, etc.

FOLDALIGN

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

FOLDALIGN is an algorithm for local simultaneous folding and aligning two or more RNA sequences.

FoldX

Wed, 16 May 2012 05:30:12 -0400

FOLD-X is a program for calculating the folding energies of proteins and for calculating the effect of a point mutation on the stability of a protein.

Footer

Thu, 17 May 2012 00:20:24 -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.

GEMS

Wed, 16 May 2012 02:30:05 -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.

GeneMark

Wed, 16 May 2012 03:00:05 -0400

The GeneMark family of programs employ Markov models and are specifically tuned for gene prediction for sequences from prokaryotes, viral genomes and eukaryotes.

GenePath2

Wed, 16 May 2012 19:50:08 -0400

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

GeneSeeker

Wed, 16 May 2012 11:10:06 -0400

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

GEPAS

Wed, 16 May 2012 08:50:06 -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.

GFINDer

Wed, 16 May 2012 01:10:19 -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.

Glyprot

Sun, 13 May 2012 09:00:09 -0400

Glyprot is a tool for predicting and modelling all potential N-glycosylation sites in a given 3D structure.

GoPubMed

Wed, 16 May 2012 06:40:07 -0400

GoPubMed is a tool that allows users to explore the results of PubMed queries in the context of Gene Ontology (GO) terms.

GPCRsclass

Wed, 16 May 2012 04:40:19 -0400

GPCRsclass is a tool for predicting amine-binding receptors based on a protein sequence provided by the user.

GPS

Mon, 14 May 2012 19:10:10 -0400

Using datasets of known phosphorylation sites, the Group based Phosphorylation Scoring method (GPS) allows the prediction of kinase specific phosphorylation sites from primary protein sequences.

GRIFFIN

Thu, 17 May 2012 01:10:07 -0400

GRIFFIN (G-protein-Receptor Interacting Feature Finding INstrument) uses a support vector machine and hidden markov model to predict G-protein coupled receptors (GPCRs) and G-protein coupling selectivity.

H++

Sat, 12 May 2012 17:10:11 -0400

H++ is a tool for the prediction of protonation states and pK of ionizable groups in macromolecular structures.

HHpred

Tue, 15 May 2012 11:50:06 -0400

Based on the comparison of profile HMMs, HHpred takes a protein sequence or multiple sequence alignment as input and searches for remote homologues in an assortment of databases such as PDB, SMART and Pfam. The user can select either a local or global alignment method, and the search results can be used to generate 3D structural models.

I-Mutant2.0

Tue, 15 May 2012 01:40:05 -0400

I-Mutant2.0 is a tool that can predict the effect of a single point mutation on protein stability from protein sequences or protein structures.

I2I-SiteEngine

Wed, 16 May 2012 00:40:06 -0400

Interface-to-Interface (I2I)-SiteEngine compares pairs of interacting protein binding sites by recognizing similarity of physico-chemical properties and shapes in the protein-protein interfaces.

ICGEBnet Protein Tools

Wed, 16 May 2012 22:30:07 -0400

ICGEBnet Protein Tools is a resource for analysis of 3D protein structures including domain predictors, a protein fold similiarity server (PRIDE), and tools for calculating atom protusion (CX) and/or depth (DPX) indexes in 3D models.

InterProScan

Wed, 16 May 2012 21:40:08 -0400

InterProScan allows you to query using different protein signature recognition methods to look up InterPro annotations for your sequence. These annotations results often include gene ontology terms that you can associate with your sequence.

ISTECH SNPAnalyzer

Wed, 16 May 2012 21:10:07 -0400

ISTECH SNPAnalyzer is a tool for the statistical analysis of SNP data that includes Hardy Weinberg equilibrium (HWE), haplotype estimation, linkage disequilibrium (LD), and QTL analyses. Registration required; some browser requirements and set-up necessary.

JCat

Mon, 14 May 2012 06:10:08 -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.

KinasePhos

Tue, 15 May 2012 01:00:05 -0400

KinasePhos is a tool for identifying kinase-specific phosphorylation sites in protein sequences.

Kinefold

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

Kinefold calculates (and animates) the folding kinetics of RNA sequences including pseudoknots.

LitMiner

Mon, 14 May 2012 12:00:08 -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.

MaM

Wed, 16 May 2012 09:40:08 -0400

The Multiple alignment Manipulator (MaM) takes a multiple alignment of genomic sequences as input and calculates the locations of exons, common repeat elements and unique regions based on user-selected programs/information. The graphical display also allows users to focus an assessment of sequence variation on the identified regions.

MEDock

Wed, 16 May 2012 15:40:07 -0400

MEDock (Maximum-Entropy based Docking) is a tool for predicting ligand binding sites.

MICheck

Wed, 16 May 2012 13:20:10 -0400

MICheck (Microbial Genome Checker) allows the user to verify gene annotations in previously published microbial genomes.

MicroInspector

Wed, 16 May 2012 18:20:07 -0400

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

MIDAW

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

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

miRU

Wed, 16 May 2012 14:50:09 -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.

MLST

Wed, 16 May 2012 21:50:18 -0400

MLST (Multi Locus Sequence Typing) is a nucleotide sequence based approach for the unambiguous characterisation of isolates of bacteria and other organisms using the sequences of internal fragments of seven house-keeping genes.

MovieMaker

Sun, 13 May 2012 23:30:12 -0400

MovieMaker is a web server that accepts PDB files or PDB accession numbers as input and allows short (~10 sec) downloadable movies to be generated of protein motions and interactions.

MRS

Sat, 12 May 2012 20:40:06 -0400

MRS is a biological data retrieval system that can be accessed over the web, or installed and used locally. MRS indexes several flat-file data sets for searching, including EMBL nucleotide, UniProt, PDB and KEGG. Searches can be performed globally, or on one or more flat file fields per data set.

MutDB

Thu, 17 May 2012 02:20:09 -0400

MutDB is a database that associates protein structural information with mutations and polymorphisms in gene sequences. The data is derived from dbSNP and Swiss-Prot, and can be browsed by gene name or searched by keyword or by various identifiers.

nsSNPAnalyzer

Mon, 14 May 2012 11:40:07 -0400

nsSNPAnalyzer is a tool to predict whether a nonsynonymous single nucleotide polymorphism (nsSNP) is phenotypically neutral or disease associated.

OligoWiz

Tue, 15 May 2012 15:50:04 -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.

One-Block CYRCA

Tue, 15 May 2012 08:30:11 -0400

One-Block CYRCA is a program for identifying blocks (local ungapped profiles of the most conserved regions of protein families and domains) in a multiple sequence alignment based on the LAMA and CYRCA block-to-block alignment methods.

Onto-Tools

Wed, 16 May 2012 09:00:09 -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.

ParAlign

Wed, 16 May 2012 22:10:12 -0400

ParAlign provides a service for sequence similarity searching powered by parallel computing technology. The two comparison algorithms used are Smith-Waterman and ParAlign (a heuristic method for sequence alignment).

PatchDock

Sun, 13 May 2012 01:50:10 -0400

PatchDock is an algorithm for molecular docking. The input is two molecules of any type: proteins, DNA, peptides, drugs. The output is a list of potential complexes sorted by shape complementarity criteria.

Pathway Explorer

Wed, 16 May 2012 15:00:15 -0400

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

Pathway extraction

Sun, 13 May 2012 10:10:05 -0400

The pathway extraction tool is a part of the network analysis tool suite (NeAT). Given a metabolic network, the tool extracts a subnetwork that connects a list of input compounds, reactions, EC numbers or enzyme-coding genes. Three metabolic networks (KEGG LIGAND, KEGG RPAIR and MetaCyc) are preloaded, but custom networks can be submitted as well.

PatMatch

Mon, 14 May 2012 21:20:39 -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.

PCE

Mon, 14 May 2012 12:00:17 -0400

PCE (Protein Continuum Electrostatics) is an interface to electrostatic potentials and pKa calculations using the MEAD package.

Pcleavage

Tue, 15 May 2012 06:00:10 -0400

Pcleavage is a tool that uses a support vector machine to predict immunoproteasome and constitutive proteasome cleavage sites in antigenic sequences.

pdbFun

Thu, 17 May 2012 00:20:11 -0400

pdbFun allows the user to search the PDB as a database of annotated residues. One can limit the search by annotations such as domains, binding sites, active sites, solvent exposure and residue type.

PEPVAC

Wed, 16 May 2012 07:00:05 -0400

PEPVAC is a tool to assist in the development of multi-epitope vaccines. It is optimized for this task by predicting peptides with the ability to bind to several human leukocyte antigens that have similar peptide binding specificity.

PhyloDome

Wed, 16 May 2012 21:40:10 -0400

PhyloDome is a tool with which you can visualize and analyze the phylogenetic distribution of one or more eukaryotic domains.

PISCES

Wed, 16 May 2012 21:50:05 -0400

PISCES (Protein Sequence Culling Server) allows the user to weed out sequences from a set in order to obtain a subset of relatively high PDB structure quality and/or mutual sequence identity.

POCO

Mon, 14 May 2012 23:30:11 -0400

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

POPSCOMP

Wed, 16 May 2012 17:40:06 -0400

POPSCOMP is a system for analysing the interaction between components of complexes based on calculations of the accessible surface that is buried when the complex is formed.

POWER

Wed, 16 May 2012 19:30:05 -0400

The Phylogenetic Web Repeater (POWER) allows users to perform phylogenetic analysis using the PHYLIP package. The POWER pipeline can start with processing either multiple sequence alignments (MSA) or can proceed directly with aligned sequences.

PPG

Sat, 12 May 2012 14:20:04 -0400

The Protein Picture Generator (PPG) is a tool for making pictures (and animations) of protein structures from PDB files.

PRALINE

Tue, 15 May 2012 15:50:09 -0400

Praline is a multiple sequence alignment program that can integrate information from sequence similarity searches and secondary structure prediction.

PriFi

Wed, 16 May 2012 20:00:13 -0400

PriFi is a tool for designing and evaluating primer pairs based on the input of a DNA sequence alignment; useful for the PCR amplification of homologs.

PRISM

Wed, 16 May 2012 19:20:11 -0400

PRISM (PRotein Interactions by Structural Matching) is a tool for analysing protein interfaces and predicting protein-protein interactions.

PRODOC

Mon, 14 May 2012 12:30:04 -0400

PRODOC is a repository of domain assignments from Pfam for proteins encoded in different complete genomes and a tool for querying this information.

ProFunc

Wed, 16 May 2012 06:30:06 -0400

ProFunc takes a PDB-format structure as input and predicts the likely function of the protein based on various sequence and structural analysis methods.

Projector 2

Thu, 17 May 2012 00:20:24 -0400

Projector 2 allows users to map completed portions of the genome sequence of an organism onto the finished (or unfinished) genome of a closely-related species or strain. Using the related genome sequence as a template can facilitate sequence assembly and the sequencing of the remaining gaps.

PromoterPlot

Tue, 15 May 2012 06:50:11 -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.

ProTeus

Tue, 15 May 2012 21:20:07 -0400

ProTeus (Protein Terminus) is an archive of functional signatures in protein termini

Protinfo

Wed, 16 May 2012 21:20:09 -0400

Protinfo takes a protein sequence as input and returns the atomic coordinates for a prediction of tertiary structure for that protein. Predictions can be made by comparative or de novo modelling.

QuasiMotiFinder

Sat, 12 May 2012 19:20:08 -0400

QuasiMotiFinder uses physicochemical similarity to PROSITE motifs and evolutionary conservation to predict sequence locations with possible function (pseudo-motifs).

RACE

Mon, 14 May 2012 15:40:05 -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.

REPPER

Wed, 16 May 2012 15:10:17 -0400

REPPER (REPeats and their PERiodicities) is a tool for detecting and analysing regions in protein sequences or sequence alignements that have short gapless repeats.

RibEx

Sat, 12 May 2012 14:30:10 -0400

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

RNALOSS

Tue, 15 May 2012 05:30:08 -0400

RNALOSS (RNA locally optimal secondary structure) is a tool for the computation of locally optimal secondary structures.

RPBS

Thu, 17 May 2012 00:30:14 -0400

Ressource Parisienne en Bioinformatique Structurale (RPBS) is a structural bioinformatics resource with several types of specific services including tools for searching sequence (AUTOMAT) and structure (YAKUSA) databases and for homology modelling (WLOOP).

SCANMOT

Mon, 14 May 2012 15:10:08 -0400

SCANMOT is a sequence similarity searching tool that adds the additional constraints of simultaneous matching of multiple motifs.

SCMD

Wed, 16 May 2012 17:20:04 -0400

The Sacharomyces Cerevisiae Morphological Database (SCMD) is a collection of micrographs of budding yeast mutants; visualization and data mining tools are provided.

Scooby-domain

Sun, 13 May 2012 23:10:12 -0400

Scooby-domain (sequence hydrophobicity predicts domains) is a method to identify globular domains in protein sequence, based on the observed lengths and hydrophobicities of domains from proteins with known tertiary structure.

SCRATCH

Wed, 16 May 2012 17:40:18 -0400

SCRATCH is a suite of protein structure software and servers for the prediction of secondary structure, solvent accessibility, disulphide bridges, stability effects of single amino acid mutations, disordered regions, domains, beta-residue and beta-strand pairings, amino acid contact maps, and tertiary structure.

SCR_FIND

Sun, 13 May 2012 22:20:08 -0400

SCR_FIND is a tool to analyze structurally conserved regions (SCRs) from superimposed structures and multiple sequence alignments.

SEARCHGTr

Tue, 15 May 2012 07:50:15 -0400

SEARCHGTr is a tool for the analysis of glycosyltransferases (GTrs) that allows you to compare a query sequence with the sequences of characterized GTrs.

Servers at University College London

Thu, 10 May 2012 03:30:08 -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.

SiteEngine

Mon, 14 May 2012 01:30:12 -0400

SiteEngine is a server that searches protein structures for regions that can potentially function as binding sites by scanning for regions on the surface of one protein structure that resemble a specific binding site on the other.

snoGPS

Tue, 15 May 2012 09:00:05 -0400

snoGPS allows you to search for H/ACA snoRNA (small nucleolar RNA) genes in a genomic sequence

snoscan

Wed, 16 May 2012 11:30:07 -0400

Snoscan allows you to search for C/D box methylation guide snoRNA (small nucleolar RNA) genes in a genomic sequence

SNP Cutter

Tue, 15 May 2012 07:40:11 -0400

SNP Cutter is a tool that automates PCR-RFLP assay design for SNP genotyping.

SPACE

Tue, 15 May 2012 18:00:11 -0400

SPACE (Structure Prediction and Analysis based on Complementarity with Environment) is a suite of tools for predicting and analyzing structures of biomolecules and their complexes.

Sride

Mon, 14 May 2012 23:10:08 -0400

Sride is a tool for identificating stabilizing residues in protein structure.

STING Millenium

Wed, 16 May 2012 05:00:21 -0400

STING is a suite of tools for the analysis of protein sequence, structure, stability and function - and the relationships between them.

Stitchprofiles.uio.no

Fri, 11 May 2012 08:10:06 -0400

Stitchprofiles.uio.no is a server that performs web-based computations on DNA melting. In addition to creating stitch profile diagrams representing the alternative conformations that partly melted DNA can adopt, the server can also plot the classical melting curves, probability profiles, and temperature profiles.

SymmDock

Thu, 17 May 2012 02:30:16 -0400

SymmDock is an server for prediction of complexes with cyclically symmetry by geometry based molecular docking.

SynoR

Wed, 16 May 2012 09:30:03 -0400

SynoR searches vertebrate genomes for synonymous regulatory elements.

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.

T-Reg Comparator

Tue, 15 May 2012 07:00:06 -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).

TMBETA-NET

Tue, 15 May 2012 15:50:07 -0400

Tool that predicts transmembrane beta strands in an outer membrane protein from its amino acid sequence.

TOUCAN 2

Sun, 13 May 2012 08:00:17 -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.

TRAMPLE

Mon, 14 May 2012 10:30:04 -0400

TRAMPLE is a tool for the prediction of transmembrane helices, transmembrane strands, secondary structure, and signal peptides.

tRNAscan-SE

Wed, 16 May 2012 23:50:14 -0400

tRNAscan-SE allows you to search for tRNA genes in genomic sequence. (site hosted by Lowe Lab at UCSC)

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.

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.

WebProAnalyst

Wed, 16 May 2012 08:10:19 -0400

WebProAnalyst is a tool for searching for residues whose substitutions are correlated with variations in protein activity. Key physicochemical characteristics of these sites can be calculated.

WikiGene

Tue, 15 May 2012 06:30:11 -0400

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

WordSpy

Mon, 14 May 2012 10:40:11 -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.

YASS

Wed, 16 May 2012 22:50:14 -0400

YASS performs local alignments of DNA sequences. It is available through a web interface and as a standalone command-line tool.