mkESA: enhanced suffix array construction tool

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 const...

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Detalles Bibliográficos
Autores principales: Homann, Robert, Fleer, David, Giegerich, Robert, Rehmsmeier, Marc
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2009
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2666816/
https://www.ncbi.nlm.nih.gov/pubmed/19246510
http://dx.doi.org/10.1093/bioinformatics/btp112
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author Homann, Robert
Fleer, David
Giegerich, Robert
Rehmsmeier, Marc
author_facet Homann, Robert
Fleer, David
Giegerich, Robert
Rehmsmeier, Marc
author_sort Homann, Robert
collection PubMed
description 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
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spelling pubmed-26668162009-04-29 mkESA: enhanced suffix array construction tool Homann, Robert Fleer, David Giegerich, Robert Rehmsmeier, Marc Bioinformatics Applications Note 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 Oxford University Press 2009-04-15 2009-02-26 /pmc/articles/PMC2666816/ /pubmed/19246510 http://dx.doi.org/10.1093/bioinformatics/btp112 Text en © 2009 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ 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.
spellingShingle Applications Note
Homann, Robert
Fleer, David
Giegerich, Robert
Rehmsmeier, Marc
mkESA: enhanced suffix array construction tool
title mkESA: enhanced suffix array construction tool
title_full mkESA: enhanced suffix array construction tool
title_fullStr mkESA: enhanced suffix array construction tool
title_full_unstemmed mkESA: enhanced suffix array construction tool
title_short mkESA: enhanced suffix array construction tool
title_sort mkesa: enhanced suffix array construction tool
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2666816/
https://www.ncbi.nlm.nih.gov/pubmed/19246510
http://dx.doi.org/10.1093/bioinformatics/btp112
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AT rehmsmeiermarc mkesaenhancedsuffixarrayconstructiontool

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