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Nucleic Acids Research 2005 33(Web Server Issue):W493-W495; doi:10.1093/nar/gki462
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© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

SNPServer: a real-time SNP discovery tool

David Savage1, Jacqueline Batley1, Tim Erwin1,2, Erica Logan1,2, Christopher G. Love1,2, Geraldine A. C. Lim1,2, Emmanuel Mongin1,2, Gary Barker3, German C. Spangenberg1,2 and David Edwards1,2,*

1Plant Biotechnology Centre, La Trobe University Bundoora 3086, Victoria, Australia 2Victorian Bioinformatics Consortium, Plant Biotechnology Centre, Primary Industries Research Victoria, La Trobe University Bundoora 3086, Victoria, Australia 3School of Biological Sciences, University of Bristol Bristol BS8 1UG, UK

*To whom correspondence should be addressed. Tel: +61 3 9479 5633; Fax: +61 3 9479 3618; Email: Dave.Edwards{at}dpi.vic.gov.au

Received February 11, 2005. Revised March 23, 2005. Accepted April 13, 2005.

SNPServer is a real-time flexible tool for the discovery of SNPs (single nucleotide polymorphisms) within DNA sequence data. The program uses BLAST, to identify related sequences, and CAP3, to cluster and align these sequences. The alignments are parsed to the SNP discovery software autoSNP, a program that detects SNPs and insertion/deletion polymorphisms (indels). Alternatively, lists of related sequences or pre-assembled sequences may be entered for SNP discovery. SNPServer and autoSNP use redundancy to differentiate between candidate SNPs and sequence errors. For each candidate SNP, two measures of confidence are calculated, the redundancy of the polymorphism at a SNP locus and the co-segregation of the candidate SNP with other SNPs in the alignment. SNPServer is available at http://hornbill.cspp.latrobe.edu.au/snpdiscovery.html.


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