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

Lucia Conde, Juan Vaquerizas, Hernán Dopazo, Leonardo Arbiza, Joke Reumers, Frederic Rousseau, Joost Schymkowitz, Joaquin Dopazo

    Research output: Contribution to journalArticlepeer-review

    188 Citations (Scopus)


    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.
    Original languageEnglish
    Pages (from-to)621-625
    Number of pages5
    JournalNucleic Acids Research
    Publication statusPublished - 1 Jun 2006


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