Nucleic Acids Research Advance Access originally published online on November 28, 2006
Nucleic Acids Research 2007 35(Database issue):D674-D679; doi:10.1093/nar/gkl990
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Nucleic Acids Research, 2007, Vol. 35, Database issue D674-D679
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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GeneSpeed: protein domain organization of the transcriptome
Barbara Davis Center for Childhood Diabetes, University of Colorado at Denver and Health Sciences Center 1775 North Ursula Street, Mail Stop B140, PO Box 6511, Denver, CO, 80045, USA
*To whom correspondence should be addressed. Tel: +1 303 724 6844; Fax: +1 303 724 6830; Email: jan.jensen{at}uchsc.edu
Received August 15, 2006. Revised October 27, 2006. Accepted October 30, 2006.
The GeneSpeed database (http://genespeed.uchsc.edu/) is an online database and resource tool facilitating the detailed study of protein domain homology in the transcriptomes of Homo sapiens, Mus musculus, Drosophila melanogaster and Caenorhabditis elegans. The population schema for the GeneSpeed database takes advantage of HOWARDTM parallel cluster technology (http://www.massivelyparallel.com/) and performs exhaustive tBLASTn searches covering all pre-assigned PFAM domain classes in all species (currently 7973 domain families) against the respective Unigene EST databases of the selected four transcriptomes. The resulting database provides a complete annotation of presumed protein domain presence for each Unigene cluster. To complement this domain annotation we have also performed a custom transcription factor-family curation of all Pfam domains, incorporated the Gene Ontology classifications for these domains as well as integrated the Novartis SymAtlas2 dataset for both human and mouse which provides rapid and easy access to tissue-based expression analysis. Consequently, the GeneSpeed database provides the user with the capability to browse or search the database by any of these specialized criteria as well as more traditional means (gene identifier, gene symbol, etc.), thereby enabling a supervised analysis of gene families through a top-down hierarchical basis defined by domain content, all directly linked to an optimized gene expression dataset.
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