La Folie, Quo Vadis, Evo-Devo?

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:

1. Gene SNP Consequences

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

2. dbSNP and HapMap data

SNPnexus retrieves links to dbSNP (http://www.ncbi.nlm.nih.gov/projects/SNP/) (Sherry et al 2001) and related genotypes or alleles frequency estimation from the HapMap populations (http://www.hapmap.org/) (The International HapMap Consortium 2007).