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Res Microbiol. 2008 Jun;159(5):406-14. doi: 10.1016/j.resmic.2008.03.005. Epub 2008 Apr 18.

Unifying classical and molecular taxonomic classification: analysis of the Podoviridae using BLASTP-based tools.

Author information

1
Laboratory of Gene Technology, Katholieke Universiteit Leuven, Kasteelpark Arenberg 21, Leuven, B-3001, Belgium.

Abstract

We defined phage genera by measuring genome relationships by the numbers of shared homologous/orthologous proteins. We used BLAST-based tools (CoreExtractor.vbs and CoreGenes) to analyze 55 fully sequenced bacteriophage genomes from the NCBI and EBI databases. This approach was first applied to the T7-related phages. Using a cut-off score of 40% homologous proteins, we identified three genera within the T7-related phages, redefined the phi29-related phages, and introduced five novel genera. The T7- and phi29-related phages were given subfamily status and named "Autographivirinae" and "Picovirinae", respectively. Our results confirm and refine the ICTV phage classification, enable elimination of errors in public databases, and provide a straightforward tool for the molecular classification of new phage genomes.

PMID:
18555669
DOI:
10.1016/j.resmic.2008.03.005
[Indexed for MEDLINE]

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