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NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes
T Z DeSantis1, P Hugenholtz, K Keller
1Lawrence Berkeley National Laboratory, Center for Environmental Biotechnology, Berkeley, CA, USA.
Nucleic Acids Research
|July 18, 2006
Summary
An online tool now efficiently aligns thousands of 16S rRNA genes using the Nearest Alignment Space Termination (NAST) algorithm. This simplifies bacterial and archaeal diversity analysis for researchers of all experience levels.
Area of Science:
- Microbiology
- Bioinformatics
- Computational Biology
Background:
- High-throughput analysis of bacterial and archaeal diversity requires aligning numerous 16S rRNA gene sequences.
- Existing computational demands and bioinformatics expertise hinder large-scale sequence alignment.
Purpose of the Study:
- To develop an accessible online tool for efficient multiple sequence alignment (MSA) of thousands of 16S rRNA genes.
- To leverage the Nearest Alignment Space Termination (NAST) algorithm for high-throughput microbial diversity analysis.
Main Methods:
- Implementation of a web-interface tool utilizing the NAST algorithm.
- Comparison of user-submitted sequences against the Greengenes 'Core Set' for alignment templating.
- Automated orientation, gap character insertion, and removal of non-16S data.
Main Results:
- Successful development of an online tool for aligning large sets of 16S rRNA genes.
- The tool efficiently processes thousands of sequences, creating multiple sequence alignments (MSAs).
- Generated MSAs facilitate distance matrix calculation for diversity estimates and taxonomic classification.
Conclusions:
- The NAST-based online tool democratizes high-throughput microbial community profiling.
- Researchers can now easily obtain bacterial and archaeal community profiles regardless of bioinformatics expertise.
- This advancement supports broader ecological and evolutionary studies of microbial communities.
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