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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 41 links

Displaying 15 links

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.

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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

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

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

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

CBS DAS protein viewerTool Content

http://www.cbs.dtu.dk/cgi-bin/das

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.

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

DNA > Annotations
Expression > Gene Regulation
Human Genome > Annotations
Protein > Interactions, Pathways, 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.

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

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.

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/

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.

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tagsanimals bacterial genome base sequence cattle computational biology database management systems dna sequence analysis dogs fungal genome gene expression genetic databases genetic polymorphism genetic variation genome genomics human genome humans invertebrates mice nucleic acid databases nucleic acid regulatory sequences plant genome protein databases proteins rats reference standards rna sequence alignment species specificity synteny systems integration tertiary protein structure transcriptional regulatory elements

FeatureExtractTool Content

http://www.cbs.dtu.dk/services/FeatureExtract/

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.

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/

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.

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tagscomputational biology database management systems factual databases fungal genes gene expression regulation genetic databases genome genomics humans programming languages

Human Genome Variation NomenclatureResource Content

http://www.hgvs.org/rec.html

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.

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IBM Bioinformatics and Pattern Discovery GroupTool Content

http://cbcsrv.watson.ibm.com/Tspd.html

DNA > Annotations
DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
RNA > Motifs
Sequence Comparison > Multiple Sequence Alignments

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.

NAR Web Server Issue 2003NAR Web Server Issue 2004
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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals anti-infective agents archaeal genes archaeal genome automated pattern recognition bacterial genes bacterial genome base sequence biomedical engineering chemical dictionaries computational biology conserved sequence dna dna sequence analysis eukaryotic cells evaluation studies as topic factual databases gene expression genetic databases genome genomics histones humans initiator codon leghemoglobin molecular models molecular sequence data open reading frames peptides probability protein databases protein sequence analysis proteins proteome rna sequence analysis secondary protein structure sequence alignment sequence analysis ubiquitin viral genome

Tags associated with subcategory 'Human Genome/Annotations'

humans genetic databases animals computational biology genomics systems integration algorithms database management systems dna sequence analysis sequence alignment proteins nucleic acid databases mice protein databases base sequence genome genes protein sequence analysis human genome gene expression profiling dna automated pattern recognition archaeal genome archaeal genes sequence tagged sites anti-infective agents single nucleotide polymorphism bacterial genes genetic markers chemical dictionaries biomedical engineering bacterial genome human chromosomes computer-assisted image processing protein interaction mapping University of Manchester gene expression regulation online systems protein conformation signal transduction eukaryotic cells energy metabolism transcription factors computer simulation systems biology proteomics oligonucleotide array sequence analysis phylogeny game theory evaluation studies as topic conserved sequence messenger rna codon automation ubiquitin california rna sequence analysis viral genome sequence homology tertiary protein structure phenotype National Center for Biotechnology Information (NCBI) chromosome mapping vertebrates molecular models sequence analysis secondary protein structure leghemoglobin gene frequency initiator codon histones factual databases gene expression genetic heterogeneity programming languages probability proteome peptides open reading frames software design rats molecular sequence data terminology as topic united states histocompatibility antigens class ii b-lymphocyte gene rearrangement genetic recombination histocompatibility antigens class i mutation documentation amino acid motifs BioMart nucleic acid regulatory sequences t-lymphocyte gene rearrangement skin natural language processing periodicals as topic muscles data mining indel mutation binding sites