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Open Access Highly Accessed Research article

Phamerator: a bioinformatic tool for comparative bacteriophage genomics

Steven G Cresawn1*, Matt Bogel2, Nathan Day1, Deborah Jacobs-Sera2, Roger W Hendrix2 and Graham F Hatfull2

Author affiliations

1 Department of Biology, James Madison University, 820 Madison Dr. MSC 7801, Harrisonburg, VA, 22807 USA

2 Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, 4249 5th Avenue, Pittsburgh, PA, 15260 USA

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Citation and License

BMC Bioinformatics 2011, 12:395  doi:10.1186/1471-2105-12-395

Published: 12 October 2011

Abstract

Background

Bacteriophage genomes have mosaic architectures and are replete with small open reading frames of unknown function, presenting challenges in their annotation, comparative analysis, and representation.

Results

We describe here a bioinformatic tool, Phamerator, that assorts protein-coding genes into phamilies of related sequences using pairwise comparisons to generate a database of gene relationships. This database is used to generate genome maps of multiple phages that incorporate nucleotide and amino acid sequence relationships, as well as genes containing conserved domains. Phamerator also generates phamily circle representations of gene phamilies, facilitating analysis of the different evolutionary histories of individual genes that migrate through phage populations by horizontal genetic exchange.

Conclusions

Phamerator represents a useful tool for comparative genomic analysis and comparative representations of bacteriophage genomes.