Article

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

Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO, USA.
Bioinformatics (Impact Factor: 4.98). 11/2009; 26(2):266-7. DOI: 10.1093/bioinformatics/btp636
Source: PubMed

ABSTRACT

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

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Available from: Todd Z DeSantis
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    • "We randomly sub-sampled (rarified) the resulting OTUs to 1,212 sequence per sample for both Roche 454 and Ion Torrent. Representative sequences for each were aligned to 16S reference sequences with PyNAST (Caporaso et al., 2010b). The resultant multiple sequence alignment was used to infer a phylogenetic tree with FastTree Price et al., 2010. "
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    • "We clustered the remaining sequences into OTUs at the 97% level using UPARSE (Edgar, 2013). We aligned representative sequences using PYNAST (Caporaso et al., 2010a) against the Greengenes core set (DeSantis et al., 2006). We assigned OTUs to taxonomic groups using UCLUST (Edgar, 2010) with the Greengenes representative set of sequences as reference. "
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    • "We compared the sequences and analyzed the changes in bacterial ecology using Quantitative Insights Into Microbial Ecology (QIIME; http://qiime.sourceforge.net), Bayesian, PyNAST, and UniFrac767778. The Shannon diversity index H = –Sp i ln(p i ) and Shannon equitability index E H = H/ln(S), where p i is the proportion of the ith taxonomic unit (OTU or species) and S is the total number of taxonomic units, were calculated using Microsoft Excel. "
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