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Gene. 2005 Dec 30;364:63-73. Epub 2005 Aug 29.

Automatic gene collection system for genome-scale overview of G-protein coupled receptors in eukaryotes.

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1
Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), AIST Waterfront Bio-IT Research Building 10F, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan.

Abstract

We have developed an automatic system for identifying GPCR (G-protein coupled receptor) genes from various kinds of genomes, which is finally deposited in the SEVENS database (http://sevens.cbrc.jp/), by integrating such software as a gene finder, a sequence alignment tool, a motif and domain assignment tool, and a transmembrane helix predictor. SEVENS enables us to perform a genome-scale overview of the "GPCR universe" using sequences that are identified with high accuracy (99.4% sensitivity and 96.6% specificity). Using this system, we surveyed the complete genomes of 7 eukaryotes and 224 prokaryotes, and found that there are 4 to 1016 GPCR genes in the 7 eukaryotes, and only a total of 16 GPCR genes in all the prokaryotes. Our preliminary results indicate that 11 subfamilies of the Class A family, the Class 2(B) family, the Class 3(C) family and the fz/smo family are commonly found among human, fly, and nematode genomes. We also analyzed the chromosomal locations of the GPCR genes with the Kolmogorov-Smirnov test, and found that species-specific families, such as olfactory, taste, and chemokine receptors in human and nematode chemoreceptor in worm, tend to form clusters extensively, whereas no significant clusters were detected in fly and plant genomes.

PMID:
16126348
DOI:
10.1016/j.gene.2005.05.038
[Indexed for MEDLINE]

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