title: A web-based restriction endonuclease tool for mycobacteriophage cluster prediction.
abstract: A recent explosion in the amount of genomic data has revealed a large genetic diversity in the bacteriophages that infect Mycobacterium smegmatis. In an effort to assess the novelty of newly described mycobacteriophage isolates and provide a preliminary determination of their probable cluster assignment prior to full genome sequencing, we have developed a systematic approach that relies on restriction endonuclease analysis. We demonstrate that a web-based tool, the Phage Enzyme Tool (or PET), is capable of rapidly facilitating this analysis and exhibits reliability in the putative placement of mycobacteriophages into specific clusters of previously sequenced phages. We propose that this tool represents a useful analytical step in the initial study of phage genomes and that this tool will increase the efficiency of phage genome characterization and enhance the educational activities involving mycobacteriophage discovery.
authors.affiliation: Department of Basic Pharmaceutical Sciences, College of Pharmacy, University of Louisiana at Monroe, Monroe, LA, USA.
authors.forename: Chris R
authors.initials: CR
authors.lastname: Gissendanner
authors.forename: Allison M D
authors.initials: AM
authors.lastname: Wiedemeier
authors.forename: Paul D
authors.initials: PD
authors.lastname: Wiedemeier
authors.forename: Russell L
authors.initials: RL
authors.lastname: Minton
authors.forename: Swapan
authors.initials: S
authors.lastname: Bhuiyan
authors.forename: Jeremy S
authors.initials: JS
authors.lastname: Harmson
authors.forename: Ann M
authors.initials: AM
authors.lastname: Findley
mesh_terms: D016000:Cluster Analysis; D004262:DNA Restriction Enzymes / Q000378:metabolism*; D004279:DNA, Viral / Q000032:analysis; D005819:Genetic Markers; D020407:Internet; D009160:Mycobacteriophages / Q000145:classification / Q000235:genetics; D020102:Mycobacterium smegmatis / Q000821:virology; D012984:Software
chemical_list: D004279:DNA, Viral; D005819:Genetic Markers; D004262:DNA Restriction Enzymes
keywords: Bioinformatics; Mycobacteriophage; Mycobacterium smegmatis; Phage enzyme tool (PET); Restriction endonuclease analysis