PyNAST: a flexible tool for aligning sequences to a template alignment

Motivation: The Nearest Alignment Space Termination (NAST) tool is commonly used in sequence-based microbial ecology community analysis, but due to the limited portability of the original implementation, it has not been as widely adopted as possible. Python Nearest Alignment Space Termination (PyNAS...

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Detalles Bibliográficos
Autores principales: Caporaso, J. Gregory, Bittinger, Kyle, Bushman, Frederic D., DeSantis, Todd Z., Andersen, Gary L., Knight, Rob
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2010
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2804299/
https://www.ncbi.nlm.nih.gov/pubmed/19914921
http://dx.doi.org/10.1093/bioinformatics/btp636
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author Caporaso, J. Gregory
Bittinger, Kyle
Bushman, Frederic D.
DeSantis, Todd Z.
Andersen, Gary L.
Knight, Rob
author_facet Caporaso, J. Gregory
Bittinger, Kyle
Bushman, Frederic D.
DeSantis, Todd Z.
Andersen, Gary L.
Knight, Rob
author_sort Caporaso, J. Gregory
collection PubMed
description Motivation: The Nearest Alignment Space Termination (NAST) tool is commonly used in sequence-based microbial ecology community analysis, but due to the limited portability of the original implementation, it has not been as widely adopted as possible. Python Nearest Alignment Space Termination (PyNAST) is a complete reimplementation of NAST, which includes three convenient interfaces: a Mac OS X GUI, a command-line interface and a simple application programming interface (API). Results: The availability of PyNAST will make the popular NAST algorithm more portable and thereby applicable to datasets orders of magnitude larger by allowing users to install PyNAST on their own hardware. Additionally because users can align to arbitrary template alignments, a feature not available via the original NAST web interface, the NAST algorithm will be readily applicable to novel tasks outside of microbial community analysis. Availability: PyNAST is available at http://pynast.sourceforge.net. Contact: rob.knight@colorado.edu
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spelling pubmed-28042992010-01-12 PyNAST: a flexible tool for aligning sequences to a template alignment Caporaso, J. Gregory Bittinger, Kyle Bushman, Frederic D. DeSantis, Todd Z. Andersen, Gary L. Knight, Rob Bioinformatics Applications Note Motivation: The Nearest Alignment Space Termination (NAST) tool is commonly used in sequence-based microbial ecology community analysis, but due to the limited portability of the original implementation, it has not been as widely adopted as possible. Python Nearest Alignment Space Termination (PyNAST) is a complete reimplementation of NAST, which includes three convenient interfaces: a Mac OS X GUI, a command-line interface and a simple application programming interface (API). Results: The availability of PyNAST will make the popular NAST algorithm more portable and thereby applicable to datasets orders of magnitude larger by allowing users to install PyNAST on their own hardware. Additionally because users can align to arbitrary template alignments, a feature not available via the original NAST web interface, the NAST algorithm will be readily applicable to novel tasks outside of microbial community analysis. Availability: PyNAST is available at http://pynast.sourceforge.net. Contact: rob.knight@colorado.edu Oxford University Press 2010-01-15 2009-11-13 /pmc/articles/PMC2804299/ /pubmed/19914921 http://dx.doi.org/10.1093/bioinformatics/btp636 Text en © The Author(s) 2009. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5/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/2.5) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Note
Caporaso, J. Gregory
Bittinger, Kyle
Bushman, Frederic D.
DeSantis, Todd Z.
Andersen, Gary L.
Knight, Rob
PyNAST: a flexible tool for aligning sequences to a template alignment
title PyNAST: a flexible tool for aligning sequences to a template alignment
title_full PyNAST: a flexible tool for aligning sequences to a template alignment
title_fullStr PyNAST: a flexible tool for aligning sequences to a template alignment
title_full_unstemmed PyNAST: a flexible tool for aligning sequences to a template alignment
title_short PyNAST: a flexible tool for aligning sequences to a template alignment
title_sort pynast: a flexible tool for aligning sequences to a template alignment
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2804299/
https://www.ncbi.nlm.nih.gov/pubmed/19914921
http://dx.doi.org/10.1093/bioinformatics/btp636
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