01783nas a2200253   4500008004100000245010200041210006900143300001100212490000700223520089100230653004301121653008001164653002701244653005601271100001401327700002301341700001501364700001501379700001601394700001701410700002001427700001501447856006701462       2006                        eng d00aPupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes0 aPupaSuite finding functional single nucleotide polymorphisms for  aW621-50 v343 a<p>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.</p>10aAlgorithms Computer Graphics Databases10aMolecular Genotype Haplotypes Internet Linkage Disequilibrium *Polymorphism10aNucleic Acid Evolution10aSingle Nucleotide *Software User-Computer Interface1 aConde, L.1 aVaquerizas, J., M.1 aDopazo, H.1 aArbiza, L.1 aReumers, J.1 aRousseau, F.1 aSchymkowitz, J.1 aDopazo, J.  uhttp://nar.oxfordjournals.org/cgi/content/full/34/suppl_2/W62102075nas a2200205   4500008004100000245012600041210006900167300001100236490000700247520124100254653010501495653005601600100001401656700002301670700002101693700001901714700001501733700001501748856010601763       2005                        eng d00aPupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes0 aPupasView a visual tool for selecting suitable SNPs with putativ  aW501-50 v333 aWe 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.10aComputer Graphics Genes *Genetic Predisposition to Disease Genotype Internet Phenotype *Polymorphism10aSingle Nucleotide *Software User-Computer Interface1 aConde, L.1 aVaquerizas, J., M.1 aFerrer-Costa, C.1 ade la Cruz, X.1 aOrozco, M.1 aDopazo, J.  uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1598052202164nas a2200229   4500008004100000245009400041210006900135300001100204490000700215520128900222653008201511653001201593653009301605100001401698700002301712700001601735700002401751700002201775700001601797700001501813856010601828       2004                        eng d00aPupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level0 aPupaSNP Finder a web tool for finding SNPs with putative effect   aW242-80 v323 aWe have developed a web tool, PupaSNP Finder (PupaSNP for short), for high-throughput searching for single nucleotide polymorphisms (SNPs) with potential phenotypic effect. PupaSNP takes as its input lists of genes (or generates them from chromosomal coordinates) and retrieves SNPs that could affect the 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 (TFBS) and changes in amino acids in the proteins. The program uses the mapping of SNPs in the genome provided by Ensembl. Additionally, user-defined SNPs (not yet mapped in the genome) can be easily provided to the program. Also, additional functional information from Gene Ontology, OMIM and homologies in other model organisms is provided. In contrast to other programs already available, which focus only on SNPs with possible effect in the protein, PupaSNP includes SNPs with possible transcriptional effect. PupaSNP will be of significant help in studies of multifactorial disorders, where the use of functional SNPs will increase the sensitivity of identification of the genes responsible for the disease. The PupaSNP web interface is accessible through http://pupasnp.bioinfo.cnio.es.10aAmino Acid Substitution Binding Sites Humans Internet Phenotype *Polymorphism10aGenetic10aSingle Nucleotide RNA Splicing *Software Transcription Factors/metabolism *Transcription1 aConde, L.1 aVaquerizas, J., M.1 aSantoyo, J.1 aAl-Shahrour, Fatima1 aRuiz-Llorente, S.1 aRobledo, M.1 aDopazo, J.  uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15215388