Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2010 Jan 15;26(2):266-7.
doi: 10.1093/bioinformatics/btp636. Epub 2009 Nov 13.

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

J Gregory Caporaso  1 , Kyle Bittinger, Frederic D Bushman, Todd Z DeSantis, Gary L Andersen, Rob Knight
Affiliations

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

J Gregory Caporaso et al. Bioinformatics. .

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.

Availability: PyNAST is available at http://pynast.sourceforge.net.

PubMed Disclaimer

Figures

Fig. 1.
Fig. 1.
(A) Screenshot of the PyNAST graphical user interface for Mac OS X. (B) Runtime of PyNAST is compared with that of NAST, each running on a single processor. PyNAST has a slightly shorter per sequence runtime (slope). The candidate sequences used in this evaluation ranged from 917 to 1343 bases, with a median length of 1294. The template alignment was a Greengenes core set (dated November 8, 2007) with 7682 positions and 4938 sequences.
See this image and copyright information in PMC

References

    1. Altschul SF, et al. Basic local alignment search tool. J. Mol. Biol. 1990;215:403–410. - PubMed
    1. DeSantis TZ, et al. Greengenes, a chimera-checked 16s rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 2006a;72:5069–5072. - PMC - PubMed
    1. DeSantis TZ, et al. NAST: a multiple sequence alignment server for comparative analysis of 16s rRNA genes. Nucleic Acids Res. 2006b;34:W394–W399. - PMC - PubMed
    1. Edgar RC. Muscle: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 2004;5:113. - PMC - PubMed
    1. Katoh K, et al. Mafft version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 2005;33:511–518. - PMC - PubMed

Publication types