Journal Article

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

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

in Bioinformatics

Volume 25, issue 5, pages 563-570
Published in print March 2009 | ISSN: 1367-4803
Published online January 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp003
Host–parasite relations of bacteria and phages can be unveiled by Oligostickiness, a measure of relaxed sequence similarity

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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@fms.saitama-u.ac.jp

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  4919 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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