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

Angly, Florent, Rodriguez-Brito, Beltran, Bangor, David, McNairnie, Pat, Breitbart, Mya, Salamon, Peter, Felts, Ben, Nulton, James, Mahaffy, Joseph and Rohwer, Forest (2005) PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information. BMC Bioinformatics, 6 . doi:10.1186/1471-2105-6-41


Author Angly, Florent
Rodriguez-Brito, Beltran
Bangor, David
McNairnie, Pat
Breitbart, Mya
Salamon, Peter
Felts, Ben
Nulton, James
Mahaffy, Joseph
Rohwer, Forest
Title PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information
Journal name BMC Bioinformatics   Check publisher's open access policy
ISSN 1471-2105
Publication date 2005-03
Sub-type Article (original research)
DOI 10.1186/1471-2105-6-41
Open Access Status DOI
Volume 6
Total pages 9
Place of publication London, United Kingdom
Publisher BioMed Central
Language eng
Formatted 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.
Conclusion: 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.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ
Additional Notes Article # 41

Document type: Journal Article
Sub-type: Article (original research)
Collection: School of Chemistry and Molecular Biosciences
 
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Created: Mon, 21 Feb 2011, 14:30:14 EST