PatMaN: rapid alignment of short sequences to large databases

Summary: We present a tool suited for searching for many short nucleotide sequences in large databases, allowing for a predefined number of gaps and mismatches. The commandline-driven program implements a non-deterministic automata matching algorithm on a keyword tree of the search strings. Both que...

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Detalles Bibliográficos
Autores principales: Prüfer, Kay, Stenzel, Udo, Dannemann, Michael, Green, Richard E., Lachmann, Michael, Kelso, Janet
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2008
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2718670/
https://www.ncbi.nlm.nih.gov/pubmed/18467344
http://dx.doi.org/10.1093/bioinformatics/btn223
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author Prüfer, Kay
Stenzel, Udo
Dannemann, Michael
Green, Richard E.
Lachmann, Michael
Kelso, Janet
author_facet Prüfer, Kay
Stenzel, Udo
Dannemann, Michael
Green, Richard E.
Lachmann, Michael
Kelso, Janet
author_sort Prüfer, Kay
collection PubMed
description Summary: We present a tool suited for searching for many short nucleotide sequences in large databases, allowing for a predefined number of gaps and mismatches. The commandline-driven program implements a non-deterministic automata matching algorithm on a keyword tree of the search strings. Both queries with and without ambiguity codes can be searched. Search time is short for perfect matches, and retrieval time rises exponentially with the number of edits allowed. Availability: The C++ source code for PatMaN is distributed under the GNU General Public License and has been tested on the GNU/Linux operating system. It is available from http://bioinf.eva.mpg.de/patman. Contact: pruefer@eva.mpg.de Supplementary information: Supplementary data are available at Bioinformatics online.
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spelling pubmed-27186702009-07-31 PatMaN: rapid alignment of short sequences to large databases Prüfer, Kay Stenzel, Udo Dannemann, Michael Green, Richard E. Lachmann, Michael Kelso, Janet Bioinformatics Applications Note Summary: We present a tool suited for searching for many short nucleotide sequences in large databases, allowing for a predefined number of gaps and mismatches. The commandline-driven program implements a non-deterministic automata matching algorithm on a keyword tree of the search strings. Both queries with and without ambiguity codes can be searched. Search time is short for perfect matches, and retrieval time rises exponentially with the number of edits allowed. Availability: The C++ source code for PatMaN is distributed under the GNU General Public License and has been tested on the GNU/Linux operating system. It is available from http://bioinf.eva.mpg.de/patman. Contact: pruefer@eva.mpg.de Supplementary information: Supplementary data are available at Bioinformatics online. Oxford University Press 2008-07-01 2008-05-08 /pmc/articles/PMC2718670/ /pubmed/18467344 http://dx.doi.org/10.1093/bioinformatics/btn223 Text en © 2008 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
Prüfer, Kay
Stenzel, Udo
Dannemann, Michael
Green, Richard E.
Lachmann, Michael
Kelso, Janet
PatMaN: rapid alignment of short sequences to large databases
title PatMaN: rapid alignment of short sequences to large databases
title_full PatMaN: rapid alignment of short sequences to large databases
title_fullStr PatMaN: rapid alignment of short sequences to large databases
title_full_unstemmed PatMaN: rapid alignment of short sequences to large databases
title_short PatMaN: rapid alignment of short sequences to large databases
title_sort patman: rapid alignment of short sequences to large databases
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2718670/
https://www.ncbi.nlm.nih.gov/pubmed/18467344
http://dx.doi.org/10.1093/bioinformatics/btn223
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AT greenricharde patmanrapidalignmentofshortsequencestolargedatabases
AT lachmannmichael patmanrapidalignmentofshortsequencestolargedatabases
AT kelsojanet patmanrapidalignmentofshortsequencestolargedatabases

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