title: PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information.
abstract: BACKGROUND
  Phages, viruses that infect prokaryotes, are the most abundant microbes in the world. A major limitation to studying these viruses is the difficulty of cultivating the appropriate prokaryotic hosts. One way around this limitation is to directly clone and sequence shotgun libraries of uncultured viral communities (i.e., metagenomic analyses). PHACCS http://phage.sdsu.edu/phaccs, Phage Communities from Contig Spectrum, is an online bioinformatic tool to assess the biodiversity of uncultured viral communities. PHACCS uses the contig spectrum from shotgun DNA sequence assemblies to mathematically model the structure of viral communities and make predictions about diversity.
  
  
  RESULTS
  PHACCS builds models of possible community structure using a modified Lander-Waterman algorithm to predict the underlying contig spectrum. PHACCS finds the most appropriate structure model by optimizing the model parameters until the predicted contig spectrum is as close as possible to the experimental one. This model is the basis for making estimates of uncultured viral community richness, evenness, diversity index and abundance of the most abundant genotype.
  
  
  CONCLUSIONS
  PHACCS analysis of four different environmental phage communities suggests that the power law is an important rank-abundance form to describe uncultured viral community structure. The estimates support the fact that the four phage communities were extremely diverse and that phage community biodiversity and structure may be correlated with that of their hosts.
authors.affiliation: Ecole Supérieure de Biotechnologie de Strasbourg, Boulevard Sébastien Brandt, 67413 Illkirch, France. fangly@projects.sdsu.edu <fangly@projects.sdsu.edu>
authors.forename: Florent
authors.initials: F
authors.lastname: Angly
authors.forename: Beltran
authors.initials: B
authors.lastname: Rodriguez-Brito
authors.forename: David
authors.initials: D
authors.lastname: Bangor
authors.forename: Pat
authors.initials: P
authors.lastname: McNairnie
authors.forename: Mya
authors.initials: M
authors.lastname: Breitbart
authors.forename: Peter
authors.initials: P
authors.lastname: Salamon
authors.forename: Ben
authors.initials: B
authors.lastname: Felts
authors.forename: James
authors.initials: J
authors.lastname: Nulton
authors.forename: Joseph
authors.initials: J
authors.lastname: Mahaffy
authors.forename: Forest
authors.initials: F
authors.lastname: Rohwer
mesh_terms: D000465:Algorithms; D001435:Bacteriophages / Q000378:metabolism; D044822:Biodiversity; D019295:Computational Biology / Q000379:methods*; D020451:Contig Mapping; D004247:DNA / Q000737:chemistry; D004267:DNA Viruses; D030541:Databases, Genetic; D005814:Genes, Viral; D014644:Genetic Variation; D016679:Genome, Viral; D005838:Genotype; D020407:Internet; D008957:Models, Genetic; D015233:Models, Statistical; D025941:Protein Interaction Mapping / Q000379:methods*; D017422:Sequence Analysis, DNA; D012984:Software; D014780:Viruses / Q000378:metabolism*
chemical_list: D004247:DNA
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