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Advances in biomolecular research, coupled with rapidly increasing availability of information from multiple genome sequencing initiatives, global gene expression patterns, large scale molecular interaction experiments and genome wide association studies, have led to an exponential increase in biological data.
With the advent of multiple genome sequencing projects, entire tRNA repertoires have been identified in many genomes.
Multiple genome sequencing of closely related bacterial species can address various significant issues which range from a better understanding of forces driving microbial evolution to the design of novel vaccines.
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The increasing availability of multiple genome sequences has made comparative genomic analyses of P. aeruginosa possible.
The publication of multiple genome sequences in the G. duodenalis species complex has provided important insights into parasite biology, and made post-genomic technologies, including proteomics, significantly more accessible.
Where multiple genome sequences for one species are available, only the single top bit score from across all sequences was used in the calculation.
Multiple genome sequences for Shewanellae were selected for proof of concept, not only because of the large number of publicly available genome sequences, but also because of the potential environmental importance of these organisms [17], [18], [19], [20], [21].
Multiple genome sequences from across strains of a single species offer more fine scale resolution of genetic differences that enable tracking and identification of species and development of additional genetic markers.
These data sets are available for download (http://www.pathogenomics.sfu.ca/pathogen-associated/). Additionally, to reduce redundancy and bias in this whole genome dataset (multiple genome sequences from a particular genera or species), we repeated the analysis using a subset of genomes with a minimum evolutionary distance (substitutions/site) of 0.05 (based on a recent phylogenetic analysis [39]).
If there were multiple genome sequences from the same taxon, we included the sequence with the most data.
Multiple genome sequences are available for certain bifidobacteiral species allowing for pan-genome analysis, which is the total number of different genes encoded by a certain species [ 5].
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