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

By J. Gregory Caporaso, Kyle Bittinger, Frederic D. Bushman, Todd Z. DeSantis, Gary L. Andersen, Rob Knight, Alex Bateman. Bioinform., 2009

3,469 citations recorded by the source corpus.

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. Contact: rob.knight@colorado.edu

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/3e1a824323ab58e3597aeb6c100dbf823cd46587

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Citations in the corpus

A Filtering Method to Generate High Quality Short Reads Using Illumina Paired-End Technology (2013, methodology): “5) [9] using the default UCLUST method [10] and a 97% similarity threshold for OTU formation with minimum cluster size of 2.”
Standard methods for research on Apis mellifera gut symbionts (2013, methodology): “Jackknife support for the branching patterns in the resulting dendrogram can be calculated in QIIME (Kuczynski et al., 2011), providing an estimate of confidence in the clustering patterns.”
Conducting a Microbiome Study (2014, methodology): “The most widely used software packages are QIIME (Caporaso et al., 2010b) (http://www.qiime.org) and mothur (Schloss et al., 2009) (http://www.mothur.org).”
Seasonal shifts in the insect gut microbiome are concurrent with changes in cold tolerance and immunity (2018, methodology): “177 We used Qiime software (Caporaso et al. 2010a) on the obtained raw sequences to filter and 178 remove unique barcodes and primers, low quality reads (quality score <25 bp), short and long 179 sequences (< 200 bp; >1000 bp), zero ambiguous base calls, gaps, zero primer sequence 180 mismatch, and…”
The composition of the gut microbiota shapes the colon mucus barrier (2014, neutral): “The reads were aligned to the Greengenes Core reference alignment using PyNAST [56].”
Targeting the Microbiota-Gut-Brain Axis: Prebiotics Have Anxiolytic and Antidepressant-like Effects and Reverse the Impact of Chronic Stress in Mice. (2017, neutral): “Indeed the microbiota plays an important role in neurodevelopment, leading to alterations in gene expression in critical brain regions, and resulting in perturbation to the programming of normal social and cognitive behaviors in mice (3-6).”
Community structure and diversity of endophytic bacteria in seeds of three consecutive generations of Crotalaria pumila growing on metal mine residues (2017, methodology): “The remaining sequences were grouped into OTUs based on a 97% similarity level and following Pynast alignment (Caporaso et al. 2010b) sequences were queried against Greengenes (DeSantis et al. 2006).”