identify transcriptional regulatory SNPs in promoter regions; The Ensembl (release 42) (4) and GoldenPath (downloaded 12 December 2006) (17) databases are used to identify SNPs in other transcriptional regulatory regions (e.g. microRNA, cpgIslands); KinasePhos (as of 15 August 2007) (18), OGPET (ver. 1.0) (19) and Sulfinator (as of 15 August 2007) (20) are used to examine post-translation modification sites. In addition, genomic regions that are conserved across multiple species are identified using GoldenPath (downloaded 12 December 2006) (17), and are used as described below. The complete list of 16 integrated tools and databases is provided in Table 1. Table 1.Bioinformatics tools and databases integrated into F-SNP (Release 1.0. August 2007)Functional categoryToolURLProtein codingPolyPhen (6)http://genetics.bwh.harvard.edu/pph/data/index.htmlSIFT (7)http://blocks.fhcrc.org/sift/SIFT.htmlSNPeffect (8)http://snpeffect.vib.be/index.phpSNPs3D (9)http://www.snps3d.org/modules.php?name=SNPtargetsLS-SNP (10)http://alto.compbio.ucsf.edu/LS-SNP/Queries.htmlEnsembl (4)http://www.ensembl.org/index.htmlSplicing regulationESEfinder (11)http://rulai.cshl.edu/cgi-bin/tools/ESE3/esefinder.cgiRescueESE (12)http://genes.mit.edu/burgelab/rescue-ese/ESRSearch (13)http://ast.bioinfo.tau.ac.il/PESX (14)http://cubweb.biology.columbia.edu/pesx/Ensembl (4)http://www.ensembl.org/index.htmlTranscriptional regulationTFSearch (15)http://www.cbrc.jp/research/db/TFSEARCH.htmlConsite (16)http://asp.ii.uib.no:8090/cgi-bin/CONSITE/consite/GoldenPath (17)http://genome.ucsc.edu/Ensembl (4)http://www.ensembl.org/index.htmlPost-translationKinasePhos (18)http://kinasephos.mbc.nctu.edu.tw/OGPET (19)http://ogpet.utep.edu/Sulfinator (20)http://www.expasy.ch/tools/sulfinator/Conserved regionGoldenPath (17)http://genome.ucsc.edu/For each possible functional category into which a SNP may be classified, the table provides the tools that examine this function, and the URL from which the respective tool is available (as of August 2007). The category Conserved Region in the last row is not a functional category in-and-of itself, but is informative in determining the effect of SNPs on splicing and transcriptional regulation.
