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This article is part of the supplement: Seventh International Conference on Bioinformatics (InCoB2008)

Open Access Research

Functional analysis of novel SNPs and mutations in human and mouse genomes

Chuan-Kun Liu1, Yan-Hau Chen1, Cheng-Yang Tang1, Shu-Chuan Chang1, Yi-Jung Lin1, Ming-Fang Tsai1, Yuan-Tsong Chen12 and Adam Yao12*

Author Affiliations

1 National Genotyping Center (NGC), Academia Sinica, Taipei, Taiwan 11529, R.O.C

2 Institute of Biomedical Sciences (IBMS), Academia Sinica, Taipei, Taiwan 11529, R.O.C

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BMC Bioinformatics 2008, 9(Suppl 12):S10  doi:10.1186/1471-2105-9-S12-S10

Published: 12 December 2008

Abstract

Background

With the flood of information generated by the new generation of sequencing technologies, more efficient bioinformatics tools are needed for in-depth impact analysis of novel genomic variations. FANS (Functional Analysis of Novel SNPs) was developed to streamline comprehensive but tedious functional analysis steps into a few clicks and to offer a carefully designed presentation of results so researchers can focus more on thinking instead of typing and calculating.

Results

FANS http://fans.ngc.sinica.edu.tw/ webcite harnesses the power of public information databases and powerful tools from six well established websites to enhance the efficiency of analysis of novel variations. FANS can process any point change in any coding region or GT-AG splice site to provide a clear picture of the disease risk of a prioritized variation by classifying splicing and functional alterations into one of nine risk subtypes with five risk levels.

Conclusion

FANS significantly simplifies the analysis operations to a four-step procedure while still covering all major areas of interest to researchers. FANS offers a convenient way to prioritize the variations and select the ones with most functional impact for validation. Additionally, the program offers a distinct improvement in efficiency over manual operations in our benchmark test.