Phamerator: a bioinformatic tool for comparative bacteriophage genomics

By Steven G. Cresawn, Matt Bogel, Nathan Day, D. Jacobs-Sera, R. Hendrix, Graham F. Hatfull. BMC Bioinformatics, 2011

498 citations recorded by the source corpus.

BackgroundBacteriophage genomes have mosaic architectures and are replete with small open reading frames of unknown function, presenting challenges in their annotation, comparative analysis, and representation.ResultsWe 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.ConclusionsPhamerator represents a useful tool for comparative genomic analysis and comparative representations of bacteriophage genomes.

Subfields: Ecology, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/49afcdf8426ff5c2a80883bafb796c5494194a6b

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Citations in the corpus

Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity (2015, unknown): “To compare mycobacteriophage gene contents we grouped related genes into protein families (‘phamilies’ or ‘phams’) using Phamerator (Cresawn et al., 2011), which we modified to use kClust (Hauser et al., 2013) so as to easily accommodate the large numbers of comparisons.”
A Broadly Implementable Research Course in Phage Discovery and Genomics for First-Year Undergraduate Students (2014, unknown): “Comparative genomics used Phamerator (31) and Gepard (58).”
Evolution of Superinfection Immunity in Cluster A Mycobacteriophages (2019, methodology): “The database Actinobacteriophage_1321 was created using Phamerator (43), consisting of 1,305 manually annotated genomes of actinobacteriophages isolated from the environment and 16 engineered or isolated mutants as described below.”
Toward a Phage Cocktail for Tuberculosis: Susceptibility and Tuberculocidal Action of Mycobacteriophages against Diverse Mycobacterium tuberculosis Strains (2021, background): “Spectrum-colored shading between the genomes reflects nucleotide sequence similarity, with violet being the most similar, and red the least similar above a threshold E value of 10(24) (64).”