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

  • Attila Egri-Nagy
  • Andrew R. Francis
  • Volker Gebhardt
Conference paper

DOI: 10.1007/978-3-662-44199-2_12

Volume 8592 of the book series Lecture Notes in Computer Science (LNCS)
Cite this paper as:
Egri-Nagy A., Francis A.R., Gebhardt V. (2014) Bacterial Genomics and Computational Group Theory: The BioGAP Package for GAP. In: Hong H., Yap C. (eds) Mathematical Software – ICMS 2014. ICMS 2014. Lecture Notes in Computer Science, vol 8592. Springer, Berlin, Heidelberg

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.

Keywords

computational group theory bacterial genomics 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Attila Egri-Nagy
    • 1
  • Andrew R. Francis
    • 1
  • Volker Gebhardt
    • 1
  1. 1.Centre for Research in Mathematics, School of Computing, Engineering and MathematicsUniversity of Western SydneyAustralia