NAST: A multiple sequence alignment server for comparative analysis of 16S rRNA genes

DeSantis, T. Z., Hugenholtz, P., Keller, K., Brodie, E. L., Larsen, N., Piceno, Y. M., Phan, R. and Andersen, G. L. (2006) NAST: A multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Research, 34 suppl 2: W394-W399. doi:10.1093/nar/gkl244

Author DeSantis, T. Z.
Hugenholtz, P.
Keller, K.
Brodie, E. L.
Larsen, N.
Piceno, Y. M.
Phan, R.
Andersen, G. L.
Title NAST: A multiple sequence alignment server for comparative analysis of 16S rRNA genes
Journal name Nucleic Acids Research   Check publisher's open access policy
ISSN 0305-1048
Publication date 2006-07-01
Sub-type Article (original research)
DOI 10.1093/nar/gkl244
Open Access Status DOI
Volume 34
Issue suppl 2
Start page W394
End page W399
Total pages 6
Place of publication Oxford, United Kingdom
Publisher Oxford University Press
Language eng
Abstract 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 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.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: ERA 2012 Admin Only
School of Chemistry and Molecular Biosciences
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Created: Mon, 28 Nov 2011, 09:34:29 EST by Hong Lee on behalf of School of Chemistry & Molecular Biosciences