http://www.snp-nexus.org/index.html
SNPnexus database is designed to simplify and assist in the selection of functionally relevant Single Nucleotide Polymorphisms (SNP) for large-scale genotyping studies of multifactorial disorders.
SNPnexus allows single or batch queries using dbSNP identifiers or in-house SNPs genomic coordinates on clones, contigs or chromosomes.
SNPnexus will be updated on a regular monthly basis and will provide the scientific community with a common friendly web- interface to perform the following analyses:
A wide range of possible SNPs functional consequences is computed on the major gene annotation systems from NCBI RefSeq (Pruitt et al., 2007), UCSC Known Genes (Hsu et al 2006), Ensembl (Hubbard et al, 2007), Vega (Ashurst et al, 2005) and Acembly (Thierry-Mieg et al 2006). SNPs effects fall into 7 categories: intronic, 5’UTR, 3’UTR, 5-upstream, 3-downstream, splicing site or coding (synonymous or non-synonymous). For intronic SNPs, the distance to the splicing site is reported. For 5-upstream and 3-downstream, a distance of 2 kb from the UTR start or end is considered appropriate. For coding SNPs, the coordinates of the position within the cdna, cds, amino acid as well as the peptide change produced (if any) are reported
Overlaps with putative copy number polymorphisms (CNP) and sites of detected intermediate-sized structural variation (ISV) determined by various methods can be retrieved. These are derived from the Database of Genomic Variants (DGV) (http://projects.tcag.ca/variation/) via UCSC and cover deletions from genotype analysis using the HapMap Phase I data, release 16a (McCarroll et al 2006 ), HapMap Phase I data, release 16c.1, CEU and YRI samples (Conrad et al 2006) and from haploid hybridization analysis in 24 unrelated individuals from the Polymorphism Discovery Resource, selected for SNP LD study (Hinds et al 2006). This also include Copy Number Polymorphism (CNP) from BAC microarray analysis in a first population of 55 individuals (Iafrate et al 2004), a second population of 47 individuals (Sharp et al 2005) as well in the HapMap Phase II data (Redon et al 2006). Further CNP regions are identified using array CGH in the HapMap populations (269 individuals) (Locke et al 2006) and using Representational oligonucleotide microarray analysis (ROMA) (Sebat et al 2004) in a population of 20 normal individuals. ISV sites are detected by mapping paired-end sequences from a human fosmid DNA library (Tuzun et al 2005).
NGS (2)