Friday, January 6, 2012

Fwd: SNPdbe: Constructing an nsSNP functional impacts database

Fwd: please follow footer link
SNPdbe: Constructing an nsSNP functional impacts database:

Summary: Many existing databases annotate experimentally characterized single nucleotide polymorphisms (SNPs). Each non-synonymous SNP (nsSNP) changes one amino acid in the gene product (single amino acid substitution; SAAS). This change can either affect protein function or be neutral in that respect. Most polymorphisms lack experimental annotation of their functional impact. Here, we introduce SNPdbe - SNPdatabase of effects, with predictions of computationally annotated functional impacts of SNPs. Database entries represent nsSNPs in dbSNP and 1000 Genomes collection, as well as variants from UniProt and PMD. SAASs come from more than 2600 organisms; "human" being the most prevalent. The impact of each SAAS on protein function is predicted using the SNAP and SIFT algorithms and augmented with experimentally derived func-tion/structure information and disease associations from PMD, OMIM and UniProt. SNPdbe is consistently updated and easily augmented with new sources of information. The DB is available as a MySQL dump and via a web front-end that allows searches with any combination of organism names, sequences and mutation IDs.

Availability:http://www.rostlab.org/services/snpdbe

Contact:snpdbe@rostlab.org



(Original Post: Bioinformatics - Advance Access.)