%0 Journal Article
%T PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information
%A Florent Angly
%A Beltran Rodriguez-Brito
%A David Bangor
%A Pat McNairnie
%A Mya Breitbart
%A Peter Salamon
%A Ben Felts
%A James Nulton
%A Joseph Mahaffy
%A Forest Rohwer
%J BMC Bioinformatics
%D 2005
%I BioMed Central
%R 10.1186/1471-2105-6-41
%X 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.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.Most environmental viruses are phages (a.k.a., bacteriophages) that infect prokaryotic cells, both Bacteria and Archaea. On average there are about ten phage particles per host cell [1]. Extrapolations from the number of prokaryotes [2] make phages the most abundant biological entities in the biosphere with an estimated 1031 viral particles. By killing prokaryotes, phages can strongly impact microbial community biomass [3] and structure [4]. Despite their importance, very little is known about phage biodiversity.Traditionally, the study of environmental phage diversity, dynamics, and ecology requires growing prokaryotes on microbiology plates and infecting them with phages. However this standard technique is limited by the fact that only a small fraction of environmental microbes are readily cultured [5] and that each phage species generally only has a very narrow number of possible microbial hosts [6]. In addition, even if it is possible to observe phages with an electron microscope, pictures are not sufficient to identify species because of the low taxonomic resolution of viral morphology. Cultivating and observing phages do not permit to assess environme
%U http://www.biomedcentral.com/1471-2105/6/41