mkESA: enhanced suffix array construction tool

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 a...

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Veröffentlicht in:	Bioinformatics 2009-04, Vol.25 (8), p.1084-1085
Hauptverfasser:	Homann, Robert, Fleer, David, Giegerich, Robert, Rehmsmeier, Marc
Format:	Artikel
Sprache:	eng
Schlagworte:	Algorithms Applications Note Biological and medical sciences Computational Biology - methods Fundamental and applied biological sciences. Psychology General aspects Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Sequence Analysis - methods Sequence Analysis, DNA - methods Sequence Analysis, Protein - methods Sequence Analysis, RNA - methods Software
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Beschreibung
Zusammenfassung:	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
ISSN:	1367-4803 1460-2059 1367-4811
DOI:	10.1093/bioinformatics/btp112