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Phamerator: A bioinformatic tool for comparative bacteriophage genomics

Cresawn, SG and Bogel, M and Day, N and Jacobs-Sera, D and Hendrix, RW and Hatfull, GF (2011) Phamerator: A bioinformatic tool for comparative bacteriophage genomics. BMC Bioinformatics, 12.

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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. © 2011 Cresawn et al; licensee BioMed Central Ltd.


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Item Type: Article
Status: Published
CreatorsEmailPitt UsernameORCID
Cresawn, SG
Bogel, M
Day, N
Jacobs-Sera, Ddjs@pitt.eduDJS0000-0001-7838-3257
Hendrix, RWrhx@pitt.eduRHX
Hatfull, GFgfh@pitt.eduGFH
Date: 12 October 2011
Date Type: Publication
Journal or Publication Title: BMC Bioinformatics
Volume: 12
DOI or Unique Handle: 10.1186/1471-2105-12-395
Schools and Programs: Dietrich School of Arts and Sciences > Biological Sciences
Refereed: Yes
MeSH Headings: Bacillus Phages--genetics; Bacteriophages--genetics; Genome, Viral; Genomics--methods; Open Reading Frames; Phylogeny; Software; Streptomyces--virology
Other ID: NLM PMC3233612
PubMed Central ID: PMC3233612
PubMed ID: 21991981
Date Deposited: 16 Nov 2012 16:15
Last Modified: 27 Sep 2022 14:57


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