PhamClust: a phage genome clustering tool using proteomic equivalence.

ABSTRACT: Bacteriophage comparative genomics is complex due to the mosaic nature of the genomes, and an underlying continuum of diversity confounds the identification of clear taxonomic boundaries. Nucleotide sequence comparison methods have been described for phage taxonomy, but they are computationally intensive and scale poorly as the number of sequenced phage genomes increases. Here, we describe PhamClust as a new bioinformatic approach for grouping phages according to their inter-genome relatedness. PhamClust calculates a proteomic equivalence quotient (PEQ) for each pair of phages based on amino acid sequence identity for those genes that are shared among phages. PEQ values span from 0% (no shared genes) to 100% (all genes shared at 100% identity), and using a large mycobacteriophage genome da

SUBMITTER: Gauthier CH 

PROVIDER: S-EPMC10654103 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature