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. 2006 Jul 1;34(Web Server issue):W635-41.
doi: 10.1093/nar/gkl236.

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

Hsiang-Yu Yuan  1 , Jen-Jie Chiou, Wen-Hsien Tseng, Chia-Hung Liu, Chuan-Kun Liu, Yi-Jung Lin, Hui-Hung Wang, Adam Yao, Yuan-Tsong Chen, Chun-Nan Hsu
Affiliations

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

Hsiang-Yu Yuan et al. Nucleic Acids Res. .

Abstract

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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Figures

Figure 1
Figure 1
Decision tree for prioritizing a SNP based on its functional effects. The diamonds represent decision points and the ovals represent terminal points with the risk and class assignments. Given an input SNP at a decision point, if the answer to the question in the diamond is ‘yes,’ then the vertical arrow should be followed. Otherwise, the horizontal arrow should be followed.
Figure 2
Figure 2
FastSNP component modules and data flow. Each gray box represents an external web server accessed by a web wrapper agent, and each blue box represents a local Java program. Open boxes are data and the arrows represent the data flow.
Figure 3
Figure 3
Comparison of SNP's risk predicted by FASTSNP and their MAF. The results are obtained by analyzing 1569 SNPs from the SNP500Cancer database with FASTSNP.
See this image and copyright information in PMC

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