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. 2006 Jul 1;34(Web Server issue):W621-5.
doi: 10.1093/nar/gkl071.

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

Lucía Conde  1 , Juan M Vaquerizas, Hernán Dopazo, Leonardo Arbiza, Joke Reumers, Frederic Rousseau, Joost Schymkowitz, Joaquín Dopazo
Affiliations

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

Lucía Conde et al. Nucleic Acids Res. .

Abstract

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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Figures

Figure 1
Figure 1
Output with the graphic representation of SNPs with putative functional effect in the gene BRCA2, along with LD maps.
See this image and copyright information in PMC

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