Tetranucleotide usage in mycobacteriophage genomes: alignment-free methods to cluster phage and infer evolutionary relationships
© Siranosian et al; licensee BioMed Central Ltd. 2015
Published: 28 January 2015
The genomic sequences of phages isolated on mycobacterial hosts are diverse, mosaic and often share little nucleotide similarity. However, about 30 unique types have been isolated, allowing most phage to be grouped into clusters and further into subclusters . Many tools for the analysis of mycobacteriophage genomes depend on sequence alignment or knowledge of gene content. These methods are computationally expensive, can require significant manual input (for example, gene annotation) and can be ineffective for significantly diverged sequences . We evaluated tetranucleotide usage in mycobacteriophages as an alternative to alignment-based methods for genome analysis.
Genome analysis based on tetranucleotide usage shows promise for evaluating host-parasite coevolution and gene exchange within the mycobacteriophage population. These methods are computationally inexpensive and independent of gene annotation, making them optimal candidates for further research aimed at clustering phage and determining evolutionary relationships. Code for genome analysis and data used in this project are freely available at https://github.com/bsiranosian/tango_final.
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