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Bioinformatics Advance Access originally published online on January 6, 2009
Bioinformatics 2009 25(5):563-570; doi:10.1093/bioinformatics/btp003
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Host–parasite relations of bacteria and phages can be unveiled by Oligostickiness, a measure of relaxed sequence similarity

Shamim Ahmed , Ayumu Saito , Miho Suzuki , Naoto Nemoto and Koichi Nishigaki *

Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan

*To whom correspondence should be addressed.


  Abstract

Motivation: The recent metagenome analysis has been producing a large number of host-unassigned viruses. Although assigning viruses to their hosts is basically important not only for virology but also for prevention of epidemic, it has been a laborious and difficult task to date. The only effective method for this purpose has been to find them in a same microscopic view. Now, we tried a computational approach based on genome sequences of bacteria and phages, introducing a physicochemical parameter, SOSS (set of oligostickiness similarity score) derived from oligostickiness, a measure of binding affinity of oligonucleotides to template DNA.

Results: We could confirm host–parasite relationships of bacteria and their phages by SOSS analysis: all phages tested (25 species) had a remarkably higher SOSS value with its host than with unrelated bacteria. Interestingly, according to SOSS values, lysogenic phages such as lambda phage (host: Escherichia coli) or SPP1 (host: Bacillus subtilis) have distinctively higher similarity with its host than its non-lysogenic (excretive or virulent) ones such as fd and T4 (host: E.coli) or phages gamma and PZA (host: B.subtilis). This finding is very promising for assigning host-unknown viruses to its host. We also investigated the relationship in codon usage frequency or G+C content of genomes to interpret the phenomenon revealed by SOSS analysis, obtaining evidences which support the hypothesis that higher SOSS values resulted from the cohabitation in the same environment which may cause the common biased mutation. Thus, lysogenic phages which stay inside longer resemble the host.

Contact: koichi{at}fms.saitama-u.ac.jp

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: John Quackenbush

Received on September 4, 2008; revised on December 27, 2008; accepted on December 30, 2008

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