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NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes
1 Lawrence Berkeley National Laboratory, Center for Environmental Biotechnology Berkeley, CA, USA 2 DOE Joint Genome Institute, Microbial Ecology Program Walnut Creek, CA, USA 3 Danish Genome Institute Aarhus, Denmark 4 Lawrence Berkeley National Laboratory, Virtual Institute for Microbial Stress and Survival Berkeley, CA, USA 5 University of California, Quantitative Biomedical Research Berkeley, CA, USA
*To whom correspondence should be addressed. Email: tdesantis{at}lbl.gov
Received February 14, 2006. Revised March 8, 2006. Accepted March 29, 2006.
Microbiologists conducting surveys of bacterial and archaeal diversity often require comparative alignments of thousands of 16S rRNA genes collected from a sample. The computational resources and bioinformatics expertise required to construct such an alignment has inhibited high-throughput analysis. It was hypothesized that an online tool could be developed to efficiently align thousands of 16S rRNA genes via the NAST (Nearest Alignment Space Termination) algorithm for creating multiple sequence alignments (MSA). The tool was implemented with a web-interface at http://greengenes.lbl.gov/NAST. Each user-submitted sequence is compared with Greengenes' ‘Core Set’, comprising 
10 000 aligned non-chimeric sequences representative of the currently recognized diversity among bacteria and archaea. User sequences are oriented and paired with their closest match in the Core Set to serve as a template for inserting gap characters. Non-16S data (sequence from vector or surrounding genomic regions) are conveniently removed in the returned alignment. From the resulting MSA, distance matrices can be calculated for diversity estimates and organisms can be classified by taxonomy. The ability to align and categorize large sequence sets using a simple interface has enabled researchers with various experience levels to obtain bacterial and archaeal community profiles.
*Correspondence may also be addressed to G. L. Andersen. Tel: +1 510 495 2795; Fax: +1 510 486 7152; Email: GLAndersen{at}lbl.gov
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