Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases.

@article{citeulike:2151781, abstract = {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/.}, address = {Switch Laboratory, Department of Applied Biological Sciences, Vrije Universiteit Brussel, Switch Laboratory, VIB, Pleinlaan 2, 1050 Brussel, Belgium, Bioinformatics Department, Centro de Investigaci\'{o}n Pr\'{i}ncipe Felipe (CIPF) and Functional Genomics Node, INB, CIPF, Valencia 46013, Spain.}, author = {Reumers, Joke and Conde, Lucia and Medina, Ignacio and Maurer-Stroh, Sebastian and Durme, Joost Van V. and Dopazo, Joaquin and Rousseau, Frederic and Schymkowitz, Joost }, citeulike-article-id = {2151781}, issn = {1362-4962}, journal = {Nucleic Acids Res}, month = {December}, posted-at = {2008-06-20 15:31:29}, priority = {2}, title = {Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/18086700}, year = {2007} }

TY - JOUR ID - citeulike:2151781 L3 - citeulike-article-id:2151781 TI - Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases. JF - Nucleic Acids Res AD - Switch Laboratory, Department of Applied Biological Sciences, Vrije Universiteit Brussel, Switch Laboratory, VIB, Pleinlaan 2, 1050 Brussel, Belgium, Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF) and Functional Genomics Node, INB, CIPF, Valencia 46013, Spain. SN - 1362-4962 N2 - 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/. AU - Reumers, Joke AU - Conde, Lucia AU - Medina, Ignacio AU - Maurer-Stroh, Sebastian AU - Durme, Joost Van AU - Dopazo, Joaquin AU - Rousseau, Frederic AU - Schymkowitz, Joost PY - 2007/12/17/ UR - http://view.ncbi.nlm.nih.gov/pubmed/18086700 ER -