PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes.

TitlePupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes.
Publication TypeJournal Article
Year of Publication2005
AuthorsConde, Lucía, Vaquerizas Juan M., Ferrer-Costa Carles, de la Cruz Xavier, Orozco Modesto, and Dopazo Joaquin
JournalNucleic Acids Res
Volume33
PaginationW501-5
Date Published2005 Jul 1
ISSN1362-4962
KeywordsComputer Graphics, Genes, Genetic Predisposition to Disease, Genotype, Internet, Phenotype, Polymorphism, Single Nucleotide, Software, User-Computer Interface
Abstract

We have developed a web tool, PupasView, for the selection of single nucleotide polymorphisms (SNPs) with potential phenotypic effect. PupasView constitutes an interactive environment in which functional information and population frequency data can be used as sequential filters over linkage disequilibrium parameters to obtain a final list of SNPs optimal for genotyping purposes. PupasView is the first resource that integrates phenotypic effects caused by SNPs at both the translational and the transcriptional level. PupasView retrieves SNPs that could affect conserved regions that the cellular machinery uses for the correct processing of genes (intron/exon boundaries or exonic splicing enhancers), predicted transcription factor binding sites and changes in amino acids in the proteins for which a putative pathological effect is calculated. The program uses the mapping of SNPs in the genome provided by Ensembl. PupasView will be of much help in studies of multifactorial disorders, where the use of functional SNPs will increase the sensitivity of the identification of the genes responsible for the disease. The PupasView web interface is accessible through http://pupasview.ochoa.fib.es and through http://www.pupasnp.org.

DOI10.1093/nar/gki476
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