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Deposited research article

A Protein Similarity Approach For Detecting Prophage Regions In Bacterial Genomes

Geeta V Rao, Preeti Mehta, K V Srividhya and S Krishnaswamy

Bioinformatics Center, School of Biotechnology, Madurai Kamaraj University, Madurai - 625021, India.

author email corresponding author email

Genome Biology 2005, 6:P11doi:10.1186/gb-2005-6-10-p11

Published:	9 September 2005

This was the first version of this article to be made available publicly.

Subject areas: Microbiology and parasitology, Bioinformatics, Genome studies

Abstract

Background

Numerous completely sequenced bacterial genomes harbor prophage elements. These elements have been implicated in increasing the virulence of the host and in phage immunity. The e14 element is a defective lambdoid prophage element present at 25 min in the Escherichia coli K-12 genome. e14 is a well-characterized prophage element and has been subjected to in-depth bioinformatic analysis.

Results

A protein-based comparative approach using BLAST helped identify lambdoid-like prophage elements in a representative set of completely sequenced bacterial genomes. Twelve putative prophage regions were identified in six different bacterial genomes. Examination of the known and newly identified prophage regions suggests that on an average, the prophage elements do not seem to occur either randomly or in a uniform manner along the genome amongst genomes of the selected pathogenic organisms.

Conclusions

The protein based comparative approach can be effectively used to detect lambdoid-like prophage elements in bacterial genomes. It is possible that this method can be extended to all prophage elements and can be made automated.