Bioinformatics Links Directory : 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.

Apollo Genome Annotation and Curation Tool - (Found July 2, 2008 )

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.
http://www.fruitfly.org/annot/apollo/

Ulysses - (Found July 2, 2008 )

Ulysses is a system to annotate human genes based on gene interactions in model organisms. Data are transferred from amenable species like yeast, fly, and worm through homology, and functional gene annotation is facilitated through the framework of a large database. The system unites homology mapping through HomoloGene and the integrated database Atlas.
http://www.cisreg.ca:8080/ulysses/

UCSC Human Genome Browser Gateway - (Found July 2, 2008 )

Provides a rapid and reliable display of any requested portion of the human genome at any scale, together with dozens of aligned annotation tracks.
http://genome.ucsc.edu/cgi-bin/hgGateway?org=Human&db=0&hgsid=27735471

Pegasys: workflow management for bioinformatics - (Found July 2, 2008 )

Pegasys is a a flexible, modular and customizable software system that coordinates the execution of multiple biological sequence analysis tools and facilitates the integration of their output. The software allows users to create analysis workflows using a graphical user interface. Adaptors are included for various software tools.
http://www.bioinformatics.ubc.ca/pegasys/

NCBI Map Viewer - (Found July 2, 2008 )

The NCBI Map Viewer provides graphical displays of features on NCBI's assembly of human genomic sequence data as well as cytogenetic, genetic, physical, and radiation hybrid maps.
http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi

JAFA - (Found July 2, 2008 )

Joined Assembly of Function Annotations (JAFA) queries multiple functional annotation servers including GOblet, GOfigure, GOtcha, and InterProScan to return the gene ontology (GO) terms that are associated with your protein sequence highlighting where the results from different servers agree.
http://jafa.burnham.org/

Harvester - (Found July 2, 2008 )

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 databasesservers: UniprotSWISSprot, ensEMBL, BLAST (NCBI), SOURCE, SMART, STRING, PSORT2, CDART, UniGene and SOSUI.
http://harvester.embl.de/

H-Invitational Database - (Found July 2, 2008 )

The H-Invitational Database (H-InvDB) is a human gene database containing over 20,000 cDNA clusters from multiple high-throughput cDNA sequencing projects. The website provides a genome browser, blast searching, and searching based on information such as OMIM, GO, SCOP and HUGO IDs, chromosome number, data source and feature type. There is also an online user manual, and much of the data is downloadable in both flat file and XML formats.
http://www.h-invitational.jp/

FAN - (Found July 2, 2008 )

FAN (Fingerprint Analysis of Nucleotide sequences) searches nucleotide sequences against the PRINTS database, a collection of protein fingerprints used to assign uncharacterized sequences to known families and hence to infer tentative functions.
http://umber.sbs.man.ac.uk/cgi-bin/neil/ntfront.pl

DNannotator - (Found July 2, 2008 )

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).
http://sky.bsd.uchicago.edu/DNannotator.htm