Bacterial Genomics and Computational Group Theory: The BioGAP Package for GAP

Abstract

Bacterial genomes can be modelled as permutations of conserved regions. These regions are sequences of nucleotides that are identified for a set of bacterial genomes through sequence alignment, and are presumed to be preserved through the underlying process, whether through chance or selection. Once a correspondence is established between genomes and permutations, the problem of determining the evolutionary distance between genomes (in order to construct phylogenetic trees) can be tackled by use of group-theoretical tools. Here we review some of the resulting problems in computational group theory and describe BioGAP, a computer algebra package for genome rearrangement calculations, implemented in GAP.

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