QuickSNP:: an automated web server for selection of tagSNPs
QuickSNP:: an automated web server for selection of tagSNPs
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DOI：
10.1093/nar/gkm329
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发表时间：
2007-07-01
影响因子：
14.9
通讯作者：
Potash, James B.
中科院分区：
文献类型：
--
作者：
Grover, Deepak;Woodfield, Alonzo S.;Potash, James B.
虽然涉及数百至数千个SNP的大规模遗传关联研究已经变得可行，但相关成本很高。即使使用tagSNPs提高了效率，研究人员也经常在寻找最大化资源利用的方法，给出一组基于SNP的基因图谱目标。我们开发了一个名为QuickSNP的Web服务器，以提供具有成本效益的SNP选择，并填补了现有SNP选择工具中的一些空白。QuickSNP的一个有用的功能是可以自动选择染色体区域中以基因为中心的SNP。其他有用的特征包括编码非同义SNP的自动选择、基于SNP间距离的SNP过滤和关于SNP的基因分型测定的可用性以及它们是否存在于全基因组芯片上的信息。该程序生成用户友好的汇总表和结果，以及UCSC基因组浏览器轨道的链接，该轨道说明了所选tagSNP与基因和其他基因组特征的关系。我们希望该服务器的独特功能组合将有助于研究人员为他们的基因分型研究选择标记。该服务器是免费提供的，可以通过URL http://bioinformoodics.jhmi.edu/quickSNP.pl访问。
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.