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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 76 links

Displaying 15 links

agriGOTool Content

http://bioinfo.cau.edu.cn/agriGO/ [open in a new window]

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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.

links directory index: 63
TitlePublication YearGoogle Scholar Citation Count
agriGO: a GO analysis toolkit for the agricultural community201063
NAR Web Server Issue 2010
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AnnotQTLTool Content

http://annotqtl.genouest.org [open in a new window]

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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.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
AnnotQTL: a new tool to gather functional and comparative information on a genomic region20111
NAR Web Server Issue 2011
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tagsanimals cattle genomics humans livestock mice molecular sequence annotation quantitative trait loci

antiSMASHTool Content

http://antismash.secondarymetabolites.org [open in a new window]

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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.

links directory index: 19
TitlePublication YearGoogle Scholar Citation Count
antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences201119
NAR Web Server Issue 2011
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tagsbacteria bacterial genes bacterial genome biosynthetic pathways fungal genes fungal genome fungi genomics molecular sequence annotation peptide synthases polyketide synthases substrate specificity

Apollo Genome Annotation and Curation ToolTool Content

http://apollo.berkeleybop.org [open in a new window]

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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.

links directory index: 279
TitlePublication YearGoogle Scholar Citation Count
Apollo: a sequence annotation editor2002279
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tagsanimals database management systems humans nucleic acid databases software design

ArtemisTool Content

http://www.sanger.ac.uk/Software/Artemis/ [open in a new window]

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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.

links directory index: 1577
TitlePublication YearGoogle Scholar Citation Count
ACT: the Artemis Comparison Tool2005438
Artemis: sequence visualization and annotation20001139
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ASAPDatabase Content

https://asap.ahabs.wisc.edu/asap/home.php [open in a new window]

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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.

links directory index: 45
TitlePublication YearGoogle Scholar Citation Count
ASAP: a resource for annotating, curating, comparing, and disseminating genomic data200645
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AsteriasTool Content

http://asterias.bioinfo.cnio.es/ [open in a new window]

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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.

links directory index: 555
TitlePublication YearGoogle Scholar Citation Count
Asterias: integrated analysis of expression and aCGH data using an open-source, web-based, parallelized software suite200713
Gene selection and classification of microarray data using random forest2006485
DNMAD: web-based diagnosis and normalization for microarray data200457
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 [open in a new window]

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

links directory index: 1271
TitlePublication YearGoogle Scholar Citation Count
Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling201045
Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments200854
BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments2006215
BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments2005204
FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes2004753
NAR Web Server Issue 2005NAR Web Server Issue 2006NAR Web Server Issue 2008NAR Web Server Issue 2010
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BankItTool Content

http://www.ncbi.nlm.nih.gov/BankIt/ [open in a new window]

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DNA > Annotations
DNA > Sequence Retrieval and Submission

Web-based submission of one or a few sequences to GenBank.

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setsNational Center for Biotechnology Information (NCBI)

BASysTool Content

http://basys.ca [open in a new window]

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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.

links directory index: 78
TitlePublication YearGoogle Scholar Citation Count
BASys: a web server for automated bacterial genome annotation200578
NAR Web Server Issue 2005
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tagsbacterial chromosomes bacterial genome genomics plasmids

BeeSpace NavigatorTool Content

http://www.beespace.illinois.edu [open in a new window]

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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.

links directory index: 0
TitlePublication YearGoogle Scholar Citation Count
BeeSpace Navigator: exploratory analysis of gene function using semantic indexing of biological literature.20110
NAR Web Server Issue 2011
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tagsanimals genes medline

Bioinformatics ToolkitTool Content

http://toolkit.tuebingen.mpg.de/ [open in a new window]

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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 [open in a new window]

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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.

links directory index: 191
TitlePublication YearGoogle Scholar Citation Count
BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications201111
BioPortal: ontologies and integrated data resources at the click of a mouse2009180
NAR Web Server Issue 2009NAR Web Server Issue 2011
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external linksLink on Twitter

BioverseTool Content

http://bioverse.compbio.washington.edu/ [open in a new window]

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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.

links directory index: 95
TitlePublication YearGoogle Scholar Citation Count
Functional annotation from predicted protein interaction networks200537
BIOVERSE: enhancements to the framework for structural, functional and contextual modeling of proteins and proteomes200513
Enhanced functional information from predicted protein networks200420
Bioverse: Functional, structural and contextual annotation of proteins and proteomes200325
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/ [open in a new window]

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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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