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


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

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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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    ABSTRACT: Next generation sequencing (NGS) technology is a widely accepted tool used by microbial ecologists to explore complex microbial communities in different ecosystems. As new NGS platforms continue to become available, it becomes imperative to compare data obtained from different platforms and analyze their effect on microbial community structure. In the present study, we compared sequencing data from both the 454 and Ion Torrent (PGM) platforms on the same DNA samples obtained from the rumen of dairy cows during their transition period. Despite the substantial difference in the number of reads, error rate and length of reads among both platforms, we identified similar community composition between the two data sets. Procrustes analysis revealed similar correlations ( M 2 = 0.319; P = 0.001) in the microbial community composition between the two platforms. Both platforms revealed the abundance of the same bacterial phyla which were Bacteroidetes and Firmicutes; however, PGM recovered an additional four phyla. Comparisons made at the genus level by each platforms revealed differences in only a few genera such as Prevotella , Ruminococcus , Succiniclasticum and Treponema ( p < 0.05; chi square test). Collectively, we conclude that the output generated from PGM and 454 yielded concurrent results, provided stringent bioinformatics pipelines are employed.
    Full-text · Article · Mar 2016 · PeerJ
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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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    ABSTRACT: Coniferous forest nitrogen (N) budgets indicate unknown sources of N. A consistent association between limber pine (Pinus flexilis) and potential N2-fixing acetic acid bacteria (AAB) indicates that native foliar endophytes may supply subalpine forests with N. To assess whether the P. flexilis–AAB association is consistent across years, we re-sampled P. flexilis twigs at Niwot Ridge, CO and characterized needle endophyte communities via 16S rRNA Illumina sequencing. To investigate whether endophytes have access to foliar N2, we incubated twigs with 13N2-enriched air and imaged radioisotope distribution in needles, the first experiment of its kind using 13N. We used the acetylene reduction assay to test for nitrogenase activity within P. flexilis twigs four times from June to September. We found evidence for N2 fixation in P. flexilis foliage. N2 diffused readily into needles and nitrogenase activity was positive across sampling dates. We estimate that this association could provide 6.8–13.6 μg N m−2 d−1 to P. flexilis stands. AAB dominated the P. flexilis needle endophyte community. We propose that foliar endophytes represent a low-cost, evolutionarily stable N2-fixing strategy for long-lived conifers. This novel source of biological N2 fixation has fundamental implications for understanding forest N budgets.
    Full-text · Article · Feb 2016 · New Phytologist
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    • "We compared the sequences and analyzed the changes in bacterial ecology using Quantitative Insights Into Microbial Ecology (QIIME;, 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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    ABSTRACT: Dysbiosis is a hallmark of inflammatory bowel disease (IBD), but it is unclear which specific intestinal bacteria predispose to and which protect from IBD and how they are regulated. Peptidoglycan recognition proteins (Pglyrps) are antibacterial, participate in maintaining intestinal microflora, and modulate inflammatory responses. Mice deficient in any one of the four Pglyrp genes are more sensitive to dextran sulfate sodium (DSS)-induced colitis, and stools from Pglyrp-deficient mice transferred to wild type (WT) germ-free mice predispose them to much more severe colitis than stools from WT mice. However, the identities of these Pglyrp-regulated bacteria that predispose Pglyrp-deficient mice to colitis or protect WT mice from colitis are not known. Here we identified significant changes in β-diversity of stool bacteria in Pglyrp-deficient mice compared with WT mice. The most consistent changes in microbiome in all Pglyrp-deficient mice were in Bacteroidales, from which we selected four species, two with increased abundance (Prevotella falsenii and Parabacteroides distasonis) and two with decreased abundance (Bacteroides eggerthii and Alistipes finegoldii). We then gavaged WT mice with stock type strains of these species to test the hypothesis that they predispose to or protect from DSS-induced colitis. P. falsenii, P. distasonis, and B. eggerthii all enhanced DSS-induced colitis in both WT mice with otherwise undisturbed intestinal microflora and in WT mice with antibiotic-depleted intestinal microflora. By contrast, A. finegoldii (which is the most abundant species in WT mice) attenuated DSS-induced colitis both in WT mice with otherwise undisturbed intestinal microflora and in WT mice with antibiotic-depleted intestinal microflora, similar to the colitis protective effect of the entire normal microflora. These results identify P. falsenii, P. distasonis, and B. eggerthii as colitis-promoting species and A. finegoldii as colitis-protective species.
    Full-text · Article · Jan 2016 · PLoS ONE
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