<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Reumers, J.</style></author><author><style face="normal" font="default" size="100%">L. Conde</style></author><author><style face="normal" font="default" size="100%">Medina, Ignacio</style></author><author><style face="normal" font="default" size="100%">Maurer-Stroh, S.</style></author><author><style face="normal" font="default" size="100%">Van Durme, J.</style></author><author><style face="normal" font="default" size="100%">Dopazo, J.</style></author><author><style face="normal" font="default" size="100%">Rousseau, F.</style></author><author><style face="normal" font="default" size="100%">Schymkowitz, J.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases</style></title><secondary-title><style face="normal" font="default" size="100%">Nucleic Acids Res</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Amino Acid Substitution Animals *Databases</style></keyword><keyword><style  face="normal" font="default" size="100%">Genetic Genetic Diseases</style></keyword><keyword><style  face="normal" font="default" size="100%">Inborn/genetics HSP70 Heat-Shock Proteins/metabolism Humans Internet Mice MicroRNAs/metabolism *Mutation *Polymorphism</style></keyword><keyword><style  face="normal" font="default" size="100%">Single Nucleotide Proteins/chemistry/genetics RNA Splice Sites Rats Transcription Factors/metabolism</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D825</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">Database issue</style></number><volume><style face="normal" font="default" size="100%">36</style></volume><pages><style face="normal" font="default" size="100%">D825-9</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;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/.&lt;/p&gt;</style></abstract><notes><style face="normal" font="default" size="100%">&lt;p&gt;Reumers, Joke Conde, Lucia Medina, Ignacio Maurer-Stroh, Sebastian Van Durme, Joost Dopazo, Joaquin Rousseau, Frederic Schymkowitz, Joost Research Support, Non-U.S. Gov’t England Nucleic acids research Nucleic Acids Res. 2008 Jan;36(Database issue):D825-9. Epub 2007 Dec 17.&lt;/p&gt;</style></notes></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">L. Conde</style></author><author><style face="normal" font="default" size="100%">Vaquerizas, J. M.</style></author><author><style face="normal" font="default" size="100%">H. Dopazo</style></author><author><style face="normal" font="default" size="100%">Arbiza, L.</style></author><author><style face="normal" font="default" size="100%">Reumers, J.</style></author><author><style face="normal" font="default" size="100%">Rousseau, F.</style></author><author><style face="normal" font="default" size="100%">Schymkowitz, J.</style></author><author><style face="normal" font="default" size="100%">Dopazo, J.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes</style></title><secondary-title><style face="normal" font="default" size="100%">Nucleic Acids Res</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Algorithms Computer Graphics Databases</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Genotype Haplotypes Internet Linkage Disequilibrium *Polymorphism</style></keyword><keyword><style  face="normal" font="default" size="100%">Nucleic Acid Evolution</style></keyword><keyword><style  face="normal" font="default" size="100%">Single Nucleotide *Software User-Computer Interface</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2006</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://nar.oxfordjournals.org/cgi/content/full/34/suppl_2/W621</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">Web Server issue</style></number><volume><style face="normal" font="default" size="100%">34</style></volume><pages><style face="normal" font="default" size="100%">W621-5</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;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.&lt;/p&gt;</style></abstract><notes><style face="normal" font="default" size="100%">&lt;p&gt;Conde, Lucia Vaquerizas, Juan M Dopazo, Hernan Arbiza, Leonardo Reumers, Joke Rousseau, Frederic Schymkowitz, Joost Dopazo, Joaquin Research Support, Non-U.S. Gov’t England Nucleic acids research Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W621-5.&lt;/p&gt;</style></notes></record></records></xml>