mkESA: enhanced suffix array construction tool

Homann R, Fleer D, Giegerich R, Rehmsmeier M (2009)
Bioinformatics 25(8): 1084-1085.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Abstract / Bemerkung
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.
Erscheinungsjahr
2009
Zeitschriftentitel
Bioinformatics
Band
25
Ausgabe
8
Seite(n)
1084-1085
ISSN
1367-4803
eISSN
1460-2059
Page URI
https://pub.uni-bielefeld.de/record/1634374

Zitieren

Homann R, Fleer D, Giegerich R, Rehmsmeier M. mkESA: enhanced suffix array construction tool. Bioinformatics. 2009;25(8):1084-1085.
Homann, R., Fleer, D., Giegerich, R., & Rehmsmeier, M. (2009). mkESA: enhanced suffix array construction tool. Bioinformatics, 25(8), 1084-1085. doi:10.1093/bioinformatics/btp112
Homann, R., Fleer, D., Giegerich, R., and Rehmsmeier, M. (2009). mkESA: enhanced suffix array construction tool. Bioinformatics 25, 1084-1085.
Homann, R., et al., 2009. mkESA: enhanced suffix array construction tool. Bioinformatics, 25(8), p 1084-1085.
R. Homann, et al., “mkESA: enhanced suffix array construction tool”, Bioinformatics, vol. 25, 2009, pp. 1084-1085.
Homann, R., Fleer, D., Giegerich, R., Rehmsmeier, M.: mkESA: enhanced suffix array construction tool. Bioinformatics. 25, 1084-1085 (2009).
Homann, Robert, Fleer, David, Giegerich, Robert, and Rehmsmeier, Marc. “mkESA: enhanced suffix array construction tool”. Bioinformatics 25.8 (2009): 1084-1085.

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