mkESA: enhanced suffix array construction tool

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

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Zeitschriftenaufsatz | Veröffentlicht | Englisch
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.
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Zeitschriftentitel
Bioinformatics
Band
25
Zeitschriftennummer
8
Seite
1084-1085
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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.

7 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

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12 References

Daten bereitgestellt von Europe PubMed Central.

Replacing suffix trees with enhanced suffix arrays
Abouelhoda M., 2004
Fast index based algorithms and software for matching position specific scoring matrices
Beckstette M., 2006
Optimal spliced alignments of short sequence reads.
De Bona F, Ossowski S, Schneeberger K, Ratsch G., Bioinformatics 24(16), 2008
PMID: 18689821
Efficient implementation of lazy suffix trees
Giegerich R., 2003

Gusfield D., 1997
Efficient multiple genome alignment.
Hohl M, Kurtz S, Ohlebusch E., Bioinformatics 18 Suppl 1(), 2002
PMID: 12169561
Gepard: a rapid and sensitive tool for creating dotplots on genome scale.
Krumsiek J, Arnold R, Rattei T., Bioinformatics 23(8), 2007
PMID: 17309896
Suffix Arrays: a new method for on-line string searches
Manber U, Myers E., 1993
Two space saving tricks for linear time LCP array computation
Manzini G., 2004
Engineering a lightweight suffix array construction algorithm
Manzini G, Ferragina P., 2004
A taxonomy of suffix array construction algorithms
Puglisi SJ., 2007

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