Differentiation of regions with atypical oligonucleotide composition in bacterial genomes

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 acquired gene islands or ancient regions such as genes for ribosomal proteins and RNAs. OU statistical parameters, such as local pattern deviation (D), pattern skew (PS) and OU variance (OUV) enabled the detection and...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Oleg N. Reva, Burkhard Tümmler
• Keywords: Atypical Oligonucleotide Composition, Bacterial Genomes, BMCBI 2005, Oligonucleotide Usage