title: PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes.
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.
authors.affiliation: Department of Bioinformatics, Centro de Investigación Príncipe Felipe (CIPF), Valencia, 46013, Spain.
authors.forename: Lucía
authors.initials: L
authors.lastname: Conde
authors.forename: Juan M
authors.initials: JM
authors.lastname: Vaquerizas
authors.forename: Hernán
authors.initials: H
authors.lastname: Dopazo
authors.forename: Leonardo
authors.initials: L
authors.lastname: Arbiza
authors.forename: Joke
authors.initials: J
authors.lastname: Reumers
authors.forename: Frederic
authors.initials: F
authors.lastname: Rousseau
authors.forename: Joost
authors.initials: J
authors.lastname: Schymkowitz
authors.forename: Joaquín
authors.initials: J
authors.lastname: Dopazo
mesh_terms: D000465:Algorithms; D003196:Computer Graphics; D030561:Databases, Nucleic Acid; D019143:Evolution, Molecular; D005838:Genotype; D006239:Haplotypes; D020407:Internet; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide; D012984:Software; D014584:User-Computer Interface