The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
PyNAST: a flexible tool for aligning sequences to a template alignment
Open accessAbstract
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
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Cites
Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., Keller, K., Huber, T., Dalevi, D., Hu, P., & Andersen, G. L. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.03006-05 · Cited by 10,891
Self-citation
Research works printed but not linked: 5
- DeSantis, 2006, NAST: a multiple sequence alignment server for comparative analysis of 16s rRNA genes, Nucleic Acids Res., 34, W394, 10.1093/nar/gkl244 · DOI · Paper page
- Edgar, 2004, Muscle: a multiple sequence alignment method with reduced time and space complexity, BMC Bioinformatics, 5, 113, 10.1186/1471-2105-5-113 · DOI
- Katoh, 2005, Mafft version 5: improvement in accuracy of multiple sequence alignment, Nucleic Acids Res., 33, 511, 10.1093/nar/gki198 · DOI · Paper page
- Knight, 2007, PyCogent: a toolkit for making sense from sequence, Genome Biol., 8, R171, 10.1186/gb-2007-8-8-r171 · DOI
- Thompson, 1994, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Res., 22, 4673, 10.1093/nar/22.22.4673 · DOI · Paper page
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Self-citationGut microbiota composition correlates with diet and health in the elderly
Claesson, M. J., Jeffery, I. B., Conde, S., Power, S. E., O’Connor, E. M., Cusack, S., Harris, H. M. B., Coakley, M., Lakshminarayanan, B., O’Sullivan, O., et al. (2012) · Nature · doi:10.1038/nature11319 · Cited by 3,314
Metadata
- Authors
- Caporaso, J. G., Bittinger, K., Bushman, F. D., DeSantis, T. Z., Andersen, G. L., & Knight, R.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-11-13
- Volume
- 26
- Issue
- 2
- Pages
- 266-267
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2104318549
- Cited by
- 3,396
- References
- 2
- FWCI
- 12.84
- Type
- journal article
- Language
- en
- Open access
- hybrid
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