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Annotations

This section contains links related to annotations of the human genome. Different sites provide automated and curated annotations. See also DNA: Sequence Features and DNA: Gene Prediction.

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Found 42 links

Displaying 15 links

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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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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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

CARGOTool Content

http://cargo2.bioinfo.cnio.es/docs/aboutCargo.html [open in a new window]

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

links directory index: 18
TitlePublication YearGoogle Scholar Citation Count
CARGO: a web portal to integrate customized biological information200718
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

CBS DAS protein viewerTool Content

http://www.cbs.dtu.dk/cgi-bin/das [open in a new window]

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Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
Protein > Localization and Targeting
Protein > Sequence Features

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

links directory index: 23
TitlePublication YearGoogle Scholar Citation Count
Integrating protein annotation resources through the Distributed Annotation System200523
NAR Web Server Issue 2005
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tagsprotein sequence analysis systems integration

DAVID Bioinformatics ResourcesTool Content

http://david.abcc.ncifcrf.gov/home.jsp [open in a new window]

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DNA > Annotations
Expression > Gene Regulation
Human Genome > Annotations
Protein > Networks & Interactions, Pathways and Enzymes
Sequence Comparison > Comparative Genomics

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.

links directory index: 3468
TitlePublication YearGoogle Scholar Citation Count
DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists2007161
DAVID: Database for Annotation, Visualization, and Integrated Discovery20033307
NAR Web Server Issue 2007
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tagsalgorithms automated pattern recognition computational biology gene expression profiling genetic databases genomics hiv-1 humans macrophages mononuclear leukocytes nucleic acid databases oligonucleotide array sequence analysis statistical data interpretation

DNannotatorTool Content

http://bioapp.psych.uic.edu/DNannotator.htm [open in a new window]

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DNA > Annotations
Human Genome > Annotations

DNannotator is a tool that performs de novo annotation of SNPs, STSs, and exons. It also allows for the migration of user-defined annotations onto different versions of genomic sequences (<30Kb size limit).

This content is being maintained by cliu.

links directory index: 14
TitlePublication YearGoogle Scholar Citation Count
Frequency Finder: a multi-source web application for collection of public allele frequencies of SNP markers20047
DNannotator: Annotation software tool kit for regional genomic sequences20037
NAR Web Server Issue 2003
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tagsalgorithms dna primers dna sequence analysis gene frequency genetic databases genetic markers genomics human chromosomes human genome humans sequence alignment sequence tagged sites single nucleotide polymorphism

Ensembl Genome BrowserTool Content

http://www.ensembl.org/ [open in a new window]

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DNA > Annotations
Human Genome > Annotations
Model Organisms > General Resources
Model Organisms > Other Organisms

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

links directory index: 4071
TitlePublication YearGoogle Scholar Citation Count
Ensembl Genomes: extending Ensembl across the taxonomic space.201063
Ensembl's 10th year2010169
Ensembl 20092009558
Ensembl 20082008434
Ensembl 20072007717
Ensembl 20062006383
Ensembl 20052005460
Ensembl 20042004192
Ensembl 2002: accommodating comparative genomics2003230
The Ensembl genome database project.2002865
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FeatureExtractTool Content

http://www.cbs.dtu.dk/services/FeatureExtract/ [open in a new window]

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DNA > Annotations
DNA > Sequence Retrieval and Submission
Human Genome > Annotations
Protein > Sequence Retrieval
RNA > Sequence Retrieval

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

links directory index: 8
TitlePublication YearGoogle Scholar Citation Count
FeatureExtract--extraction of sequence annotation made easy20058
NAR Web Server Issue 2005
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tagschromosomes dna sequence analysis gene components humans nucleic acid databases

Gene Set BuilderTool Content

http://www.cisreg.ca/gsb/ [open in a new window]

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DNA > Sequence Retrieval and Submission
Human Genome > Annotations
Human Genome > Other Resources
Model Organisms > General Resources
Protein > Sequence Retrieval

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.

links directory index: 4
TitlePublication YearGoogle Scholar Citation Count
The Gene Set Builder: collation, curation, and distribution of sets of genes20054
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tagscomputational biology database management systems factual databases fungal genes gene expression regulation genetic databases genome genomics humans programming languages

HarvesterTool Content

http://harvester.fzk.de/harvester/ [open in a new window]

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Human Genome > Annotations
Protein > Annotation and Function

Harvester provides fast access to public bioinformatic databases and servers for human proteins. Results are returned as a single HTML page that contains the cached and cross-linked output from the following databases/servers: Uniprot/SWISSprot, ensEMBL, BLAST (NCBI), SOURCE, SMART, STRING, PSORT2, CDART, UniGene and SOSUI.

links directory index: 35
TitlePublication YearGoogle Scholar Citation Count
'Harvester': a fast meta search engine of human protein resources200435
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tagsdatabase management systems documentation humans natural language processing protein databases proteins systems integration

Human Genome Variation NomenclatureResource Content

http://www.hgvs.org/rec.html [open in a new window]

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Human Genome > Annotations
Human Genome > Genomics
Human Genome > Other Resources
Human Genome > Sequence Polymorphisms

The Human Genome Society has established a committee to suggest standards for the description of sequence variants in DNA, RNA, and protein sequences. The standards are linked here.

links directory index: not available
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