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Bioinformatics Advance Access published online on February 26, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp112
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

mkESA: Enhanced Suffix Array Construction Tool

Robert Homann 1,2,*, David Fleer 2, Robert Giegerich 2 and Marc Rehmsmeier 3,4

1International NRW Graduate School in Bioinformatics and Genome Research, Center for Biotechnology (CeBiTec), Bielefeld University, 33594 Bielefeld, Germany
2Technische Fakultät, Bielefeld University, Postfach 100 131, 33501 Bielefeld, Germany
3Center for Biotechnology (CeBiTec), Bielefeld University, 33594 Bielefeld, Germany
4Present address: Gregor Mendel Institute of Molecular Plant Biology GmbH, 1030 Vienna, Austria

*To whom correspondence should be addressed. Mr. Robert Homann, E-mail: rhomann{at}techfak.uni-bielefeld.de


  Abstract

Summary: We introduce the tool mkESA, an open source program for constructing enhanced suffix arrays (ESAs), striving for low memory consumption, yet high practical speed. mkESA is a userfriendly program written in portable C99, based on a parallelized version of the Deep-Shallow suffix array construction algorithm, which is known for its high speed and small memory usage. The tool handles large FASTA files with multiple sequences, and computes suffix arrays and various additional tables, such as the LCP table (longest common prefix) or the inverse suffix array, from given sequence data.

Availability: The source code of mkESA is freely available under the terms of the GNU General Public License (GPL) version 2 at http://bibiserv.techfak.uni-bielefeld.de/mkesa/.

Contact: rhomann{at}techfak.uni-bielefeld.de

Associate Editor: Dr. Limsoon Wong

Received on January 21, 2009; revised on February 19, 2009; accepted on February 20, 2009

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