Differentiation of regions with atypical oligonucleotide composition in bacterial genomes.

ABSTRACT:

Background

Complete sequencing of bacterial genomes has become a common technique of present day microbiology. Thereafter, data mining in the complete sequence is an essential step. New in silico methods are needed that rapidly identify the major features of genome organization and facilitate the prediction of the functional class of ORFs. We tested the usefulness of local oligonucleotide usage (OU) patterns to recognize and differentiate types of atypical oligonucleotide composition in DNA sequences of bacterial genomes.

Results

A total of 163 bacterial genomes of eubacteria and archaea published in the NCBI database were analyzed. Local OU patterns exhibit substantial intrachromosomal variation in bacteria. Loci with alternative OU patterns were parts of horizontally acqui

SUBMITTER: Reva ON 

PROVIDER: S-EPMC1274298 | biostudies-literature | 2005 Oct

REPOSITORIES: biostudies-literature