QuickSNP: an automated web server for selection of tagSNPs

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 S...

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Main Authors:	Grover, Deepak, Woodfield, Alonzo S., Verma, Ranjana, Zandi, Peter P., Levinson, Douglas F., Potash, James B.
Format:	Online
Language:	English
Published:	Oxford University Press 2007
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933212/

id	pubmed-1933212
recordtype	oai_dc
spelling	pubmed-19332122007-07-31 QuickSNP: an automated web server for selection of tagSNPs Grover, Deepak Woodfield, Alonzo S. Verma, Ranjana Zandi, Peter P. Levinson, Douglas F. Potash, James B. Articles 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. Oxford University Press 2007-07 2007-05-21 /pmc/articles/PMC1933212/ /pubmed/17517769 http://dx.doi.org/10.1093/nar/gkm329 Text en © 2007 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ 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.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Grover, Deepak Woodfield, Alonzo S. Verma, Ranjana Zandi, Peter P. Levinson, Douglas F. Potash, James B.
spellingShingle	Grover, Deepak Woodfield, Alonzo S. Verma, Ranjana Zandi, Peter P. Levinson, Douglas F. Potash, James B. QuickSNP: an automated web server for selection of tagSNPs
author_facet	Grover, Deepak Woodfield, Alonzo S. Verma, Ranjana Zandi, Peter P. Levinson, Douglas F. Potash, James B.
author_sort	Grover, Deepak
title	QuickSNP: an automated web server for selection of tagSNPs
title_short	QuickSNP: an automated web server for selection of tagSNPs
title_full	QuickSNP: an automated web server for selection of tagSNPs
title_fullStr	QuickSNP: an automated web server for selection of tagSNPs
title_full_unstemmed	QuickSNP: an automated web server for selection of tagSNPs
title_sort	quicksnp: an automated web server for selection of tagsnps
description	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.
publisher	Oxford University Press
publishDate	2007
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933212/
_version_	1611398597238063104

QuickSNP: an automated web server for selection of tagSNPs

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