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Nucleic Acids Research Advance Access originally published online on May 21, 2007
Nucleic Acids Research 2007 35(Web Server issue):W115-W120; doi:10.1093/nar/gkm329
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Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W115-W120
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

QuickSNP: an automated web server for selection of tagSNPs

Deepak Grover1, Alonzo S. Woodfield1, Ranjana Verma1, Peter P. Zandi1,2, Douglas F. Levinson3 and James B. Potash1,*

1Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, 2Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21287, USA and 3Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA

*To whom correspondence should be addressed. Tel: +1 410 955 2572; Fax: +1 410 502 0065; Email: jpotash{at}jhmi.edu

Received February 1, 2007. Revised April 11, 2007. Accepted April 17, 2007.

Although large-scale genetic association studies involving hundreds to thousands of SNPs have become feasible, the associated cost is substantial. Even with the increased efficiency introduced by the use of tagSNPs, researchers are often seeking ways to maximize resource utilization given a set of SNP-based gene-mapping goals. We have developed a web server named QuickSNP in order to provide cost-effective selection of SNPs, and to fill in some of the gaps in existing SNP selection tools. One useful feature of QuickSNP is the option to select only gene-centric SNPs from a chromosomal region in an automated fashion. Other useful features include automated selection of coding non-synonymous SNPs, SNP filtering based on inter-SNP distances and information regarding the availability of genotyping assays for SNPs and whether they are present on whole genome chips. The program produces user-friendly summary tables and results, and a link to a UCSC Genome Browser track illustrating the position of the selected tagSNPs in relation to genes and other genomic features. We hope the unique combination of features of this server will be useful for researchers aiming to select markers for their genotyping studies. The server is freely available and can be accessed at the URL http://bioinformoodics.jhmi.edu/quickSNP.pl.


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