SNP@Domain: a web resource of single nucleotide polymorphisms (SNPs) within protein domain structures and sequences

Abstract

The single nucleotide polymorphisms (SNPs) in conserved protein regions have been thought to be strong candidates that alter protein functions. Thus, we have developed SNP@Domain, a web resource, to identify SNPs within human protein domains. We annotated SNPs from dbSNP with protein structure-based as well as sequence-based domains: (i) structure-based using SCOP and (ii) sequence-based using Pfam to avoid conflicts from two domain assignment methodologies. Users can investigate SNPs within protein domains with 2D and 3D maps. We expect this visual annotation of SNPs within protein domains will help scientists select and interpret SNPs associated with diseases. A web interface for the SNP@Domain is freely available at http://snpnavigator.net/ and from http://bioportal.net/.

Figure 1

Search interface of SNP@Domain. The user is able to search SNP domain annotations with three inputs including (i) SNP identifier (rs number), (ii) Gene identifier (Ensembl protein ID) or name/symbol, and (iii) Domain identifier (SCOP concise classification strings ID or Pfam ID) or name.

Figure 2

An example of detail information and image maps of an SNP within protein domains. Following the user's query to the SNP (rs number = ‘rs3088308’), the SNP's detail information including chromosomal location, class, validation and alleles were displayed. And a summary of domain mapping results and a corresponding 2D image map were shown up. Four tracks of the 2D image map were displayed including (i) Pfam domain, (ii) SCOP domain, (iii) synonymous SNPs and (iv) non-synonymous SNPs within the protein. The 3D image map of the SNP is also available.