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Bioinformatics Advance Access originally published online on April 12, 2005
Bioinformatics 2005 21(12):2814-2820; 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{at}oupjournals.org

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

Rachel Karchin 1,2,3,*, Mark Diekhans 4,5, Libusha Kelly 1,2,3, Daryl J. Thomas 4,5, Ursula Pieper 1,2,3, Narayanan Eswar 1,2,3, David Haussler 4,5,6 and Andrej Sali 1,2,3

1Department of Biopharmaceutical Sciences, University of California at San Francisco San Francisco, CA 94143, USA
2Department of Pharmaceutical Chemistry, University of California at San Francisco San Francisco, CA 94143, USA
3California Institute for Quantitative Biomedical Research, University of California at San Francisco San Francisco, CA 94143, USA
4Center for Biomolecular Science and Engineering, University of California Santa at Cruz, Santa Cruz, CA 95076, USA
5California Institute for Quantitative Biomedical Research, University of California Santa at Cruz, Santa Cruz, CA 95076, USA
6Howard Hughes Medical Institute, University of California Santa at Cruz, Santa Cruz, CA 95076, USA

*To whom correspondence should be addressed.

Motivation: The NCBI dbSNP database lists over 9 million single nucleotide polymorphisms (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

Contact: rachelk{at}salilab.org

Supplementary information: http://salilab.org/LS-SNP/supp-info.pdf


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