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Nucleic Acids Research 2005 33(Web Server Issue):W501-W505; doi:10.1093/nar/gki476
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© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

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

Lucía Conde1, Juan M. Vaquerizas1, Carles Ferrer-Costa2, Xavier de la Cruz2,4, Modesto Orozco2,3,5 and Joaquín Dopazo1,6,*

1Bioinformatics Unit, Centro Nacional de Investigaciones Oncológicas (CNIO) Madrid 28029, Spain 2Molecular Modelling and Bioinformatics Unit, Institut de Recerca Biomèdica Barcelona 08028, Spain 3Structure and Modelling Node INB, Parc Científic de Barcelona Barcelona 08028, Spain 4Institució Catalana per la Recerca i Estudis Avançats (ICREA) 08018 Barcelona, Spain 5Departament de Bioquímica i Biología Molecular Facultat de Química, Universitat de Barcelona Barcelona 08028, Spain 6Functional Genomics Node, National Institute of Bioinformatics (INB) CIPF Valencia 46013, Spain

*To whom correspondence should be addressed. Email: jdopazo{at}ochoa.fib.es

Received February 14, 2005. Revised April 15, 2005. Accepted April 15, 2005.

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.

Present address: Lucia Conde, Juan M. Vaquerizas and Joaquín Dopazo, Department of Bioinformatics, Centro de Investigación Príncipe Felipe, Valencia 46013, Spain


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