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On application of directons to functional classification of genes in prokaryotes

Paper ID Volume ID Publish Year Pages File Format Full-Text
15327 1404 2008 9 PDF Available
Title
On application of directons to functional classification of genes in prokaryotes
Abstract

Functional classification of genes represents one of the most basic problems in genome analysis and annotation. Our analysis of some of the popular methods for functional classification of genes shows that these methods are not always consistent with each other and may not be specific enough for high-resolution gene functional annotations. We have developed a method to integrate genomic neighborhood information of genes with their sequence similarity information for the functional classification of prokaryotic genes. The application of our method to 93 proteobacterial genomes has shown that (i) the genomic neighborhoods are much more conserved across prokaryotic genomes than expected by chance, and such conservation can be utilized to improve functional classification of genes; (ii) while our method is consistent with the existing popular schemes as much as they are among themselves, it does provide functional classification at higher resolution and hence allows functional assignments of (new) genes at a more specific level; and (iii) our method is fairly stable when being applied to different genomes.

Keywords
Functional classification of genes; Prokaryotes; Genomic neighborhood
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On application of directons to functional classification of genes in prokaryotes
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Publisher
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 32, Issue 3, June 2008, Pages 176–184
Authors
, , , ,
Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
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Full-text PDF Download
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