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Bioinformatics Advance Access originally published online on February 26, 2009
Bioinformatics 2009 25(8):1084-1085; doi:10.1093/bioinformatics/btp112
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

mkESA: enhanced suffix array construction tool

Robert Homann 1,2,*, David Fleer 2, Robert Giegerich 2 and Marc Rehmsmeier 3,{dagger}

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

*To whom correspondence should be addressed.


  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 user-friendly 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

{dagger}Present address: GMI - Gregor Mendel Institute of Molecular Plant Biology GmbH, Dr. Bohr-Gasse 3, 1030 Vienna, Austria.

Associate Editor: Limsoon Wong

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

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