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

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

Research output: Contribution to journalArticle

2007 Citations (Scopus)

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 languageEnglish (US)
Article numberbtp636
Pages (from-to)266-267
Number of pages2
JournalBioinformatics
Volume26
Issue number2
DOIs
StatePublished - 2010
Externally publishedYes

Fingerprint

Boidae
Python
Termination
Template
Alignment
Ecology
Interfaces (computer)
Portability
Graphical user interfaces
Application programming interfaces (API)
Availability
Programming
Hardware

ASJC Scopus subject areas

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

Cite this

Caporaso, J. G., Bittinger, K., Bushman, F. D., Desantis, T. Z., Andersen, G. L., & Knight, R. (2010). PyNAST: A flexible tool for aligning sequences to a template alignment. Bioinformatics, 26(2), 266-267. [btp636]. https://doi.org/10.1093/bioinformatics/btp636

PyNAST : A flexible tool for aligning sequences to a template alignment. / Caporaso, James G; Bittinger, Kyle; Bushman, Frederic D.; Desantis, Todd Z.; Andersen, Gary L.; Knight, Rob.

In: Bioinformatics, Vol. 26, No. 2, btp636, 2010, p. 266-267.

Research output: Contribution to journalArticle

Caporaso, JG, Bittinger, K, Bushman, FD, Desantis, TZ, Andersen, GL & Knight, R 2010, 'PyNAST: A flexible tool for aligning sequences to a template alignment', Bioinformatics, vol. 26, no. 2, btp636, pp. 266-267. https://doi.org/10.1093/bioinformatics/btp636
Caporaso JG, Bittinger K, Bushman FD, Desantis TZ, Andersen GL, Knight R. PyNAST: A flexible tool for aligning sequences to a template alignment. Bioinformatics. 2010;26(2):266-267. btp636. https://doi.org/10.1093/bioinformatics/btp636
Caporaso, James G ; Bittinger, Kyle ; Bushman, Frederic D. ; Desantis, Todd Z. ; Andersen, Gary L. ; Knight, Rob. / PyNAST : A flexible tool for aligning sequences to a template alignment. In: Bioinformatics. 2010 ; Vol. 26, No. 2. pp. 266-267.
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