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

Florent Angly12, Beltran Rodriguez-Brito24, David Bangor23, Pat McNairnie2, Mya Breitbart2, Peter Salamon3, Ben Felts3, James Nulton3, Joseph Mahaffy3 and Forest Rohwer25*

Author Affiliations

1 Ecole Supérieure de Biotechnologie de Strasbourg, Boulevard Sébastien Brandt, 67413 Illkirch, France

2 Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA

3 Department of Mathematics and Statistics, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA

4 Computational Science Research Center, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA

5 Center For Microbial Sciences, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA

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BMC Bioinformatics 2005, 6:41  doi:10.1186/1471-2105-6-41

Published: 2 March 2005

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 webcite, 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.