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