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Nucleic Acids Research 2006 34(Web Server issue):W635-W641; doi:10.1093/nar/gkl236
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© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization

Hsiang-Yu Yuan1, Jen-Jie Chiou2, Wen-Hsien Tseng2, Chia-Hung Liu2, Chuan-Kun Liu3, Yi-Jung Lin3, Hui-Hung Wang1, Adam Yao1,3, Yuan-Tsong Chen1 and Chun-Nan Hsu2,*

1 Institute of Biomedical Sciences, Academia Sinica Taipei, Taiwan 2 Institute of Information Science, Academia Sinica Taipei, Taiwan 3 National Genotyping Center, Academia Sinica Taipei, Taiwan

*To whom correspondence should be addressed. Tel: +886 2 27883799x1801; Fax: +886 2 27824814; Email: chunnan{at}iis.sinica.edu.tw

Received February 15, 2006. Revised March 8, 2006. Accepted March 28, 2006.

Single nucleotide polymorphism (SNP) prioritization based on the phenotypic risk is essential for association studies. Assessment of the risk requires access to a variety of heterogeneous biological databases and analytical tools. FASTSNP (function analysis and selection tool for single nucleotide polymorphisms) is a web server that allows users to efficiently identify and prioritize high-risk SNPs according to their phenotypic risks and putative functional effects. A unique feature of FASTSNP is that the functional effect information used for SNP prioritization is always up-to-date, because FASTSNP extracts the information from 11 external web servers at query time using a team of web wrapper agents. Moreover, FASTSNP is extendable by simply deploying more Web wrapper agents. To validate the results of our prioritization, we analyzed 1569 SNPs from the SNP500Cancer database. The results show that SNPs with a high predicted risk exhibit low allele frequencies for the minor alleles, consistent with a well-known finding that a strong selective pressure exists for functional polymorphisms. We have been using FASTSNP for 2 years and FASTSNP enables us to discover a novel promoter polymorphism. FASTSNP is available at http://fastsnp.ibms.sinica.edu.tw.


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