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Nucleic Acids Research 2006 34(Web Server issue):W621-W625; doi:10.1093/nar/gkl071
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© The Author 2006. 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@oxfordjournals.org

Article

PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes

Lucía Conde1, Juan M. Vaquerizas1, Hernán Dopazo1, Leonardo Arbiza1, Joke Reumers2, Frederic Rousseau2, Joost Schymkowitz2 and Joaquín Dopazo1,3,*

1 Department of Bioinformatics, Centro de Investigación Príncipe Felipe (CIPF) Valencia, 46013, Spain 2 Switch laboratory, Flanders Interuniversity Institute for Biotechnology. (VIB), Vrije Universiteit Brussel Pleinlaan 2, 1050 Brussels, Belgium 3 Functional Genomics Node, INB CIPF Valencia 46013, Spain

*To whom correspondence should be addressed. Tel: +34 963289680; Fax: +34 963289701; Email: jdopazo{at}cipf.es

Received February 14, 2006. Revised February 23, 2006. Accepted March 3, 2006.

We have developed a web tool, PupaSuite, for the selection of single nucleotide polymorphisms (SNPs) with potential phenotypic effect, specifically oriented to help in the design of large-scale genotyping projects. PupaSuite uses a collection of data on SNPs from heterogeneous sources and a large number of pre-calculated predictions to offer a flexible and intuitive interface for selecting an optimal set of SNPs. It improves the functionality of PupaSNP and PupasView programs and implements new facilities such as the analysis of user's data to derive haplotypes with functional information. A new estimator of putative effect of polymorphisms has been included that uses evolutionary information. Also SNPeffect database predictions have been included. The PupaSuite web interface is accessible through http://pupasuite.bioinfo.cipf.es and through http://www.pupasnp.org.


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