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

J. Gregory Caporaso; Kyle Bittinger; Frederic D. Bushman; Todd Z. Desantis; Gary L. Andersen; Rob Knight

doi:10.1093/bioinformatics/btp636

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

J. Gregory Caporaso, Kyle Bittinger, Frederic D. Bushman, Todd Z. Desantis, Gary L. Andersen, Rob Knight

Research output: Contribution to journal › Article › peer-review

2553 Scopus citations

Abstract

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.

Original language	English (US)
Pages (from-to)	266-267
Number of pages	2
Journal	Bioinformatics
Volume	26
Issue number	2
DOIs	https://doi.org/10.1093/bioinformatics/btp636
State	Published - Jan 2010
Externally published	Yes

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btp636

Cite this

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abstract = "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.",

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AU - Bushman, Frederic D.

AU - Desantis, Todd Z.

AU - Andersen, Gary L.

AU - Knight, Rob

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

Abstract

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