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Bioinformatics Advance Access published online on April 12, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti442
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received February 9, 2005
Revised April 5, 2005
Accepted April 6, 2005

Article

LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources

Rachel Karchin 1*, Mark Diekhans 2, Libusha Kelly 1, Daryl J. Thomas 2, Ursula Pieper 1, Narayanan Eswar 1, David Haussler 2, and Andrej Sali 1

1 Department of Biopharmaceutical Sciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94143, USA
2 Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, CA 95076, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94143, USA

* To whom correspondence should be addressed.
Rachel Karchin, E-mail: rachelk{at}salilab.org


  Abstract

Motivation: The NCBI dbSNP database lists over 9 million SNPs in the human genome, but currently contains limited annotation information. SNPs that result in amino-acid residue changes (nsSNPs) are of critical importance in variation between individuals, including disease and drug sensitivity.

Results: We have developed LS-SNP, a genomic-scale software pipeline to annotate nsSNPs. LS-SNP comprehensively maps nsSNPs onto protein sequences, functional pathways, and comparative protein structure models and predicts positions where nsSNPs destabilize proteins, interfere with the formation of domain-domain interfaces, have an effect on protein-ligand binding, or severely impact human health. It currently annotates 28,043 validated SNPs that produce amino-acid residue substitutions in human proteins from the SwissProt/TrEMBL database. Annotations can be viewed via a web interface either in the context of a genomic region or by selecting sets of SNPs, genes, proteins, or pathways. These results are useful for identifying candidate functional SNPs within a gene, haplotype, or pathway and in probing molecular mechanisms responsible for functional impacts of nsSNPs.

Availability: http://www.salilab.org/LS-SNP.

Supplementary Information: http://www.salilab.org/LS-SNP/Supplementary-info.pdf.


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