PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information

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 LanderWaterman 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 experime...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Florent Angly, Beltran Rodriguez-Brito, David Bangor, Pat McNairnie, Mya Breitbart, Peter Salamon, Ben Felts, James Nulton, Joseph Mahaffy, Forest Rohwer
• Keywords: BMCBI 2005, Contig Spectrum, Phage Communities, Uncultured Viral Communities