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) |
|---|---|
| Article number | btp636 |
| Pages (from-to) | 266-267 |
| Number of pages | 2 |
| Journal | Bioinformatics |
| Volume | 26 |
| Issue number | 2 |
| DOIs | |
| State | Published - 2010 |
| Externally published | Yes |
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ASJC Scopus subject areas
- Biochemistry
- Molecular Biology
- Computational Theory and Mathematics
- Computer Science Applications
- Computational Mathematics
- Statistics and Probability
Cite this
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 journal › Article
}
TY - JOUR
T1 - PyNAST
T2 - A flexible tool for aligning sequences to a template alignment
AU - Caporaso, James G
AU - Bittinger, Kyle
AU - Bushman, Frederic D.
AU - Desantis, Todd Z.
AU - Andersen, Gary L.
AU - Knight, Rob
PY - 2010
Y1 - 2010
N2 - 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.
AB - 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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UR - http://www.scopus.com/inward/citedby.url?scp=75249107844&partnerID=8YFLogxK
U2 - 10.1093/bioinformatics/btp636
DO - 10.1093/bioinformatics/btp636
M3 - Article
C2 - 19914921
AN - SCOPUS:75249107844
VL - 26
SP - 266
EP - 267
JO - Bioinformatics
JF - Bioinformatics
SN - 1367-4803
IS - 2
M1 - btp636
ER -