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

J Gregory Caporaso¹, Kyle Bittinger, Frederic D Bushman

¹Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO, USA.

Bioinformatics (Oxford, England)

|November 17, 2009

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Python Nearest Alignment Space Termination (PyNAST) enhances the popular Nearest Alignment Space Termination (NAST) tool for microbial ecology. This reimplementation offers improved portability and scalability for large datasets and novel applications.

Area of Science:

Bioinformatics
Computational Biology
Microbial Ecology

Background:

The Nearest Alignment Space Termination (NAST) tool is vital for sequence-based microbial ecology.
Limited portability of the original NAST implementation hindered widespread adoption.
A complete reimplementation, Python Nearest Alignment Space Termination (PyNAST), addresses these limitations.

Purpose of the Study:

To provide a portable and scalable implementation of the NAST algorithm.
To enhance the applicability of NAST to larger datasets and novel research areas.
To offer user-friendly interfaces for broader accessibility.

Main Methods:

Complete reimplementation of the NAST algorithm in Python.
Development of a graphical user interface (GUI) for Mac OS X.

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Implementation of a command-line interface and a simple application programming interface (API).

Main Results:

PyNAST significantly improves the portability of the NAST algorithm.
Enables analysis of datasets orders of magnitude larger than previously possible.
Allows alignment to arbitrary template alignments, expanding NAST's utility beyond microbial ecology.

Conclusions:

PyNAST makes the NAST algorithm more accessible and versatile.
Facilitates advanced sequence-based analyses in microbial ecology and other fields.
Promotes wider adoption and application of the NAST methodology.