GeneSpeed: protein domain organization of the transcriptome.

GeneSpeed: protein domain organization of the transcriptome. Research Abstract Details 

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GeneSpeed: protein domain organization of the transcriptome. Abstract Text:

Alecksandr Kutchma,Nayeem Quayum,Jan Jensen,

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 HOWARD 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.

GeneSpeed: protein domain organization of the transcriptome. Publishing Authors By Initials

A Kutchma,N Quayum,J Jensen,

For similar information science: computing methodologies: software: user-computer interface research abstracts see: information science: computing methodologies: software: user-computer interface research

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GeneSpeed: protein domain organization of the transcriptome. Journal Published:

PUBLICATION TYPE: Research Support, Non-U.S. Gov

Journal: Nucleic acids research

VOLUME: 35

Page Numbers: D674-9

Journal Abbreviation: Nucleic Acids Res.

ISSN: 1362-4962

DAY: 28

MONTH: 11

YEAR: 2006

GeneSpeed: protein domain organization of the transcriptome. Information

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LANGUAGE: eng

NlmUniqueID: 411011

GeneSpeed: protein domain organization of the transcriptome. Keywords Mesh Terms:

KEYWORDS: User-Computer Interface

MESH TERMS: chemistry

Chemical & Substance for Abstract: GeneSpeed: protein domain organization of the transcriptome. Information

Substance Name: Transcription Factors

Registry Number: 0

Grant and Affiliation Information for GeneSpeed: protein domain organization of the transcriptome.

AFFILIATION: 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.

Country: England

AGENCY: United States NIDDK

GRANT: P30 DK57516

ACRONYM: DK

MEDLINETA: Nucleic Acids Res

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