Nucleic Acids Research Advance Access published online on December 17, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm979
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Database Issue |
Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases
1Switch Laboratory, Department of Applied Biological Sciences, Vrije Universiteit Brussel, 2Switch Laboratory, VIB, Pleinlaan 2, 1050 Brussel, Belgium, 3Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF) and 4Functional Genomics Node, INB, CIPF, Valencia 46013, Spain
*To whom correspondence should be addressed. Tel: +32 2 629 14 25; Fax: +32 2 629 19 63; E-mail: joost.schymkowitz{at}vub.ac.be
Correspondence may also be addressed to Frederic Rousseau. Tel: +32 2 629 14 25; Fax: +32 2 629 19 63; E-mail: frederic.rousseau{at}vub.ac.be
Received September 15, 2007. Revised October 17, 2007. Accepted October 18, 2007.
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/.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.