Title: RECOMBFLOW: a scientific workflow environment for Intragenomic Gene Conversion analysis in bacterial genomes, including the pathogen Streptococcus pyogenes

Authors: Jamal Alhiyafi, Cavitha Sabesan, Shiyong Lu, Jeffrey L. Ram

Addresses: Department of Computer Science, Wayne State University, 430 State Hall, 5143 Cass Avenue, Detroit, MI 48202, USA. ' Department of Computer Science, Wayne State University, 430 State Hall, 5143 Cass Avenue, Detroit, MI 48202, USA. ' Department of Computer Science, Wayne State University, 430 State Hall, 5143 Cass Avenue, Detroit, MI 48202, USA. ' Department of Physiology, Wayne State University, USA

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.

Keywords: bacteria; intragenomic recombination; DNA recombination; gene conversion; bacterial genomes; scientific workflows; Streptococcus pyogenes; bioinformatics; IGC; intragenomic gene conversion.

DOI: 10.1504/IJBRA.2009.022460

International Journal of Bioinformatics Research and Applications, 2009 Vol.5 No.1, pp.1 - 19

Published online: 07 Jan 2009 *

Full-text access for editors Full-text access for subscribers Purchase this article Comment on this article