title: Host-parasite relations of bacteria and phages can be unveiled by oligostickiness, a measure of relaxed sequence similarity.
abstract: BACKGROUND
  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.
authors.affiliation: Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan.
authors.forename: Shamim
authors.initials: S
authors.lastname: Ahmed
authors.forename: Ayumu
authors.initials: A
authors.lastname: Saito
authors.forename: Miho
authors.initials: M
authors.lastname: Suzuki
authors.forename: Naoto
authors.initials: N
authors.lastname: Nemoto
authors.forename: Koichi
authors.initials: K
authors.lastname: Nishigaki
mesh_terms: D001412:Bacillus subtilis / Q000235:genetics; D001419:Bacteria / Q000235:genetics*; D001435:Bacteriophages / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D004926:Escherichia coli / Q000235:genetics; D016680:Genome, Bacterial; D016679:Genome, Viral; D006790:Host-Parasite Interactions / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods