title: RECOMBFLOW: a scientific workflow environment for Intragenomic Gene Conversion analysis in bacterial genomes, including the pathogen Streptococcus pyogenes.
abstract: Intragenomic Gene Conversion (IGC) is important in the evolution of bacteria but has only been analysed computationally in a few strains of Escherichia coli. This paper describes a scientific workflow system, called RECOMBFLOW, that automates this complex procedure for the analysis of more than 400 bacterial genomes, with a median analysis time per genome of less than 5 minutes. Results show that IGC varies greatly, both between different species and among multiple genomes of the same species. We analyse for the first time the large variation of IGC in the pathogen Streptococcus pyogenes, and also in non-pathogenic bacteria.
authors.affiliation: Department of Computer Science, Wayne State University, 430 State Hall, 5143 Cass Avenue, Detroit, MI 48202, USA. alhiyafi@wayne.edu
authors.forename: Jamal
authors.initials: J
authors.lastname: Alhiyafi
authors.forename: Cavitha
authors.initials: C
authors.lastname: Sabesan
authors.forename: Shiyong
authors.initials: S
authors.lastname: Lu
authors.forename: Jeffrey L
authors.initials: JL
authors.lastname: Ram
mesh_terms: D019295:Computational Biology / Q000379:methods*; D005785:Gene Conversion; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D011995:Recombination, Genetic; D013297:Streptococcus pyogenes / Q000235:genetics* / Q000472:pathogenicity