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

TitlePupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes
Publication TypeJournal Article
Year of Publication2006
AuthorsConde, L, Vaquerizas, JM, Dopazo, H, Arbiza, L, Reumers, J, Rousseau, F, Schymkowitz, J, Dopazo, J
JournalNucleic Acids Res
KeywordsAlgorithms Computer Graphics Databases; Molecular Genotype Haplotypes Internet Linkage Disequilibrium *Polymorphism; Nucleic Acid Evolution; Single Nucleotide *Software User-Computer Interface

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.


Conde, Lucia Vaquerizas, Juan M Dopazo, Hernan Arbiza, Leonardo Reumers, Joke Rousseau, Frederic Schymkowitz, Joost Dopazo, Joaquin Research Support, Non-U.S. Gov’t England Nucleic acids research Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W621-5.