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Bioinformatics Advance Access published online on December 21, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti220
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Bioinformatics © Oxford University Press 2004; all rights reserved.
Received October 5, 2004
Revised November 18, 2004
Accepted December 12, 2004

Article

Mapping SNPs to protein sequence and structure data

A. Cavallo 1 and A. C. R. Martin 1*

1 Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT

* To whom correspondence should be addressed.
A. C. R. Martin, E-mail: andrew{at}bioinf.org.uk; a.martin@biochem.ucl.ac.uk


  Abstract

Motivation: Data on both SNPs and disease-related mutations are being collected at ever-increasing rates. To understand the structural effects of mis-sense mutations, we consider both classes under the term ‘single amino acid polymorphisms’ (SAAPs) and we wish to map these to protein structure where their effects can be analyzed. Our initial aim therefore is to create a completely automatically maintained database of SAAPs mapped to individual residues in the Protein Databank (PDB) updated as new mutations or structures become available.

Results: We present an integrated pipeline for the automated mapping of SAAP data from HGVbase to individual PDB residues. Achieving this in a completely automated and reliable manner is a complex task. Data extracted from HGVbase are mapped to EMBL entries to confirm whether the mutation occurs in an exon and, if so, where in the sequence it occurs. From there we map to SwissProt entries and thence to the Protein Databank.

Availability: The resulting database may be accessed over the web at http://www.bioinf.org.uk/saap/ or http://acrmwww.biochem.ucl.ac.uk/saap/.


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