Title: Simulation of genomic recombination and the influence of DNA sequence diversity on cluster formation and detectability of recombination: a scientific workflow method

Authors: Jamal Alhiyafi, 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 Physiology, Wayne State University, Detroit, MI 48201, USA

Abstract: The detection of recombination from DNA sequences is relevant to the understanding of evolutionary and molecular genetics. We developed a Recombination Simulation Scientific Workflow System (RSSWS) for simulating recombination and using GENECONV to test the effect of pairwise differences in a diverse population on the detectability of recombination. Decreases in recombination rate owing to pairwise differences resulted in population clusters analogous to sympatric speciation under specific conditions and decreases in detectability of recombination, a phenomenon that we call |cryptic recombination|. This computational method demonstrated the value of scientific workflow methods for analysing a complex process and data driven problem.

Keywords: DNA recombination; genomic recombination; DNA detection programmes; sympatric speciation; scientific workflow method; simulation; DNA sequences; sequence diversity; cluster formation; molecular genetics; evolutionary genetics; pairwise differences.

DOI: 10.1504/IJCBDD.2009.027585

International Journal of Computational Biology and Drug Design, 2009 Vol.2 No.1, pp.81 - 99

Published online: 02 Aug 2009 *

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