@ARTICLE{TreeBASE2Ref26190, author = {Bryan D Merrill and Andy T Ward and Julianne H Grose and Sandra Hope}, title = {Software-based analysis of bacteriophage genomes, physical ends, and packaging strategies}, year = {2016}, keywords = {}, doi = {}, url = {http://}, pmid = {}, journal = {BMC Genomics}, volume = {}, number = {}, pages = {}, abstract = {Background Phage genome analysis is a rapidly growing field. Recurrent obstacles include software access and usability, as well as genome sequences that vary in sequence orientation and/or start position. Here we describe modifications to the phage comparative genomics software program, Phamerator, provide public access to the code, and include instructions for creating custom Phamerator databases. We further report genomic analysis techniques to determine phage packaging strategies and identification of the physical ends of phage genomes. Results We report successful modification of the original Phamerator code and provide instructions and our revised code for others to repeat the work and build custom databases. We provide results of Phamerator genome maps that demonstrate obstacles in performing genomic comparisons when published genomes have an incorrect orientation or an incorrect location of the first base of the genome. We review phage packaging strategies and provide results that demonstrate identification of the genome start location and orientation using raw sequencing data and software programs such as Pause and Consed to establish the location of the physical ends of the genome. Our results include determination of exact direct terminal repeats (DTR?s), cohesive ends, as well as headful packaging pac sequences. The results from phylogenetic analysis using ClustalO and phamily circles in Phamerator demonstrate that the large terminase gene can be used to identify the packaging strategy and thereby aide in identification of the physical ends of the genome. Conclusions Using available online code, the Phamerator program can be customized and utilized to generate databases with selected genomes. Raw data from high-throughput sequencing, together with phylogenetic analyses of large terminase proteins, and custom Phamerator databases can help researchers identify packaging strategies and physical ends of phage genomes. We promote publication of phage genomes in an orientation consistent with the physical structure of the phage chromosome. } }

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