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
Descripción
Sumario: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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