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Annotations

This section contains tools and links related to genome annotation. Different sites provide automated and curated annotations. See also DNA:Gene Prediction, DNA: Sequence Features.

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Found 65 links

Displaying 15 links

agriGOTool Content

http://bioinfo.cau.edu.cn/agriGO/

DNA > Annotations
Model Organisms > Plants
Sequence Comparison > Comparative Genomics

agriGO is an integrated gene ontology analysis toolkit for the agriculture community. Supported organisms and gene identifiers were expanded over EasyGO tool, and several tools for predicting gene function are included.

NAR Web Server Issue 2010
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tagsagricultural crops plant genes

AnnotQTLTool Content

http://annotqtl.genouest.org

DNA > Annotations
DNA > Gene Prediction

AnnotQTL is a web tool for gathering functional and comparative information on a genomic region. It is designed to aggregate functional annotations from different websites by minimizing the redundancy of the information.

NAR Web Server Issue 2011
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antiSMASHTool Content

http://antismash.secondarymetabolites.org

DNA > Annotations
Model Organisms > Microbes
Sequence Comparison > Multiple Sequence Alignments

The antibiotic and Secondary Metabolite Analysis Shell (antiSMASH) is a resource for identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences.

NAR Web Server Issue 2011
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Apollo Genome Annotation and Curation ToolTool Content

http://apollo.berkeleybop.org

DNA > Annotations
Human Genome > Annotations

Apollo is a genome annotation viewer and editor. Apollo allows researchers to explore genomic annotations at many levels of detail, and to perform expert annotation curation, all in a graphical environment.

This content is being maintained by suzi.

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tagsanimals database management systems humans nucleic acid databases software design

ArtemisTool Content

http://www.sanger.ac.uk/Software/Artemis/

DNA > Annotations
Human Genome > Annotations

DNA sequence viewer and annotation tool; allows visualization of sequence features and results of analyses within the context of the sequence and its 6-frame translation; available for UNIX, Windows and Macintosh.

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tagsalgorithms base sequence chromosome mapping computer-assisted image processing dna sequence analysis factual databases molecular sequence data sequence alignment

ASAPDatabase Content

https://asap.ahabs.wisc.edu/asap/home.php

DNA > Annotations

ASAP (a systematic annotation package for community analysis of genomes) is a relational database and web interface developed to store, update and distribute genome sequence data and functional characterization. ASAP supports three levels of users: public viewers, annotators and curators.

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tagsbacterial genome genomics nucleic acid databases sequence alignment

AsteriasTool Content

http://asterias.bioinfo.cnio.es/

DNA > Annotations
Expression > Transcript Expression Analysis

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.

This content is being maintained by rdiaz02.

NAR Web Server Issue 2007
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tagsalgorithms animals automated pattern recognition automation cluster analysis computational biology computer simulation database management systems dna sequence analysis gene expression profiling genetic models genomics humans nucleic acid hybridization oligonucleotide array sequence analysis programming languages sequence alignment statistical models

BabelomicsTool Content

http://www.babelomics.org

DNA > Annotations
Expression > Gene Regulation
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes

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.

This content is being maintained by juan_aguilar.

NAR Web Server Issue 2005NAR Web Server Issue 2006NAR Web Server Issue 2008NAR Web Server Issue 2010
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tagsalgorithms animals artificial intelligence binding sites chromosome mapping dna sequence analysis gene expression profiling genes genetic databases genomics humans mice oligonucleotide array sequence analysis phylogeny proteomics rats sequence alignment systems biology systems integration transcription factors

BASysTool Content

http://basys.ca

DNA > Annotations
Model Organisms > Microbes

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.

This content is being maintained by gary.vandomselaar@gmail.com.

NAR Web Server Issue 2005
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tagsbacterial chromosomes bacterial genome genomics plasmids

BeeSpace NavigatorTool Content

http://www.beespace.illinois.edu

DNA > Annotations
Literature > Text Mining and Semantics

BeeSpace Navigator is a tool for exploratory analysis of gene function using biological literature. It is an automated version of the curation process to extract gene function.

NAR Web Server Issue 2011
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Bioinformatics ToolkitTool Content

http://toolkit.tuebingen.mpg.de/

DNA > Annotations
DNA > DNA and Genomic Analysis
DNA > Phylogeny Reconstruction
DNA > Structure and Sequence Feature Detection
DNA > Tools For the Bench
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Do-it-all Tools for Protein
Protein > Localization and Targeting
Protein > Molecular Dynamics and Docking
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
Protein > Sequence Features
Sequence Comparison > Multiple Sequence Alignments

This Toolkit is a collection of a wide range of tools and links for sequence analysis, function, and structure prediction. This resource offers convienent web interfaces for many freely available tools.

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BioPortalDatabase Content

http://bioportal.bioontology.org

DNA > Annotations
Expression > Transcript Expression Analysis
Human Genome > Annotations
Literature > Open Access Resources
Literature > Search Tools

BioPortal is a web accessible open repository of biomedical ontologies. Users may browse, search and visualize ontologies, as well as participate in the evaluation and evolution of ontology reviews by adding notes, corrections, reviews, etc. Data from other sources such as GEO, ClinicalTrials.gov and ArrayExpress may also be integrated with the ontologies.

This content is being maintained by whetzel.

NAR Web Server Issue 2009NAR Web Server Issue 2011
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tagsbiomedical research controlled vocabulary natural language processing systems integration

BioverseTool Content

http://bioverse.compbio.washington.edu/

DNA > Annotations
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Annotation and Function
Protein > Sequence Comparison
Protein > Sequence Retrieval

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

NAR Web Server Issue 2005NAR Web Server Issue 2003
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tagsamino acid sequence homology biological models chromosome mapping computer simulation energy metabolism gene expression profiling gene expression regulation molecular models protein conformation protein interaction mapping protein sequence analysis proteins proteome proteomics signal transduction

Blast2GOTool Content

http://www.blast2go.org/

DNA > Annotations
Model Organisms > Plants

The Blast2GO suite is a comprehensive bioinformatics tool for functional annotation of plant sequences and data mining on the resulting annotations, primarily based on the gene ontology (GO) vocabulary. The application supports InterPro, enzyme codes, KEGG pathways, GO direct acyclic graphs (DAGs), and GOSlim.

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CARGOTool Content

http://cargo2.bioinfo.cnio.es/docs/aboutCargo.html

DNA > Annotations
DNA > Sequence Polymorphisms
Human Genome > Annotations
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Literature > Text Mining and Semantics
Protein > Interactions, Pathways, Enzymes

CARGO (Cancer And Related Genes Online) is a portal that uses widgets to allow users to mine literature using iHOP, retrieve disease information from OMIM, visualize 3D SNPs, query protein interactions, and view summarized gene annotation information for cancer related genes in human.

NAR Web Server Issue 2007
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tagsanimals biology computational biology database management systems factual databases genetic databases humans programming languages systems integration

Tags associated with subcategory 'DNA/Annotations'

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