02702nas a2200253   4500008004100000245013300041210006900174300001100243490000700254520167500261653004701936653002901983653012302012653010502135100001602240700001402256700002002270700002102290700001802311700001502329700001702344700002002361856006702381       2008                        eng d00aJoint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases0 aJoint annotation of coding and noncoding single nucleotide polym  aD825-90 v363 a<p>Single nucleotide polymorphisms (SNPs) are, together with copy number variation, the primary source of variation in the human genome. SNPs are associated with altered response to drug treatment, susceptibility to disease and other phenotypic variation. Furthermore, during genetic screens for disease-associated mutations in groups of patients and control individuals, the distinction between disease causing mutation and polymorphism is often unclear. Annotation of the functional and structural implications of single nucleotide changes thus provides valuable information to interpret and guide experiments. The SNPeffect and PupaSuite databases are now synchronized to deliver annotations for both non-coding and coding SNP, as well as annotations for the SwissProt set of human disease mutations. In addition, SNPeffect now contains predictions of Tango2: an improved aggregation detector, and Waltz: a novel predictor of amyloid-forming sequences, as well as improved predictors for regions that are recognized by the Hsp70 family of chaperones. The new PupaSuite version incorporates predictions for SNPs in silencers and miRNAs including their targets, as well as additional methods for predicting SNPs in TFBSs and splice sites. Also predictions for mouse and rat genomes have been added. In addition, a PupaSuite web service has been developed to enable data access, programmatically. The combined database holds annotations for 4,965,073 regulatory as well as 133,505 coding human SNPs and 14,935 disease mutations, and phenotypic descriptions of 43,797 human proteins and is accessible via http://snpeffect.vib.be and http://pupasuite.bioinfo.cipf.es/.</p>10aAmino Acid Substitution Animals *Databases10aGenetic Genetic Diseases10aInborn/genetics HSP70 Heat-Shock Proteins/metabolism Humans Internet Mice MicroRNAs/metabolism *Mutation *Polymorphism10aSingle Nucleotide Proteins/chemistry/genetics RNA Splice Sites Rats Transcription Factors/metabolism1 aReumers, J.1 aConde, L.1 aMedina, Ignacio1 aMaurer-Stroh, S.1 aVan Durme, J.1 aDopazo, J.1 aRousseau, F.1 aSchymkowitz, J.  uhttp://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D82501783nas 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/W621