Journal Article

<i>mkESA</i>: enhanced suffix array construction tool

Robert Homann, David Fleer, Robert Giegerich and Marc Rehmsmeier

in Bioinformatics

Volume 25, issue 8, pages 1084-1085
Published in print April 2009 | ISSN: 1367-4803
Published online February 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp112

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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@techfak.uni-bielefeld.de

Journal Article.  1541 words. 

Subjects: Bioinformatics and Computational Biology

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