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Open Access Highly Accessed Methodology article

SNPHunter: a bioinformatic software for single nucleotide polymorphism data acquisition and management

Lin Wang1, Simin Liu23, Tianhua Niu13* and Xin Xu1

Author Affiliations

1 Program for Population Genetics, Harvard School of Public Health, Boston, MA 02115, USA

2 Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA

3 Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA

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BMC Bioinformatics 2005, 6:60  doi:10.1186/1471-2105-6-60

Published: 18 March 2005

Abstract

Background

Single nucleotide polymorphisms (SNPs) provide an important tool in pinpointing susceptibility genes for complex diseases and in unveiling human molecular evolution. Selection and retrieval of an optimal SNP set from publicly available databases have emerged as the foremost bottlenecks in designing large-scale linkage disequilibrium studies, particularly in case-control settings.

Results

We describe the architectural structure and implementations of a novel software program, SNPHunter, which allows for both ad hoc-mode and batch-mode SNP search, automatic SNP filtering, and retrieval of SNP data, including physical position, function class, flanking sequences at user-defined lengths, and heterozygosity from NCBI dbSNP. The SNP data extracted from dbSNP via SNPHunter can be exported and saved in plain text format for further down-stream analyses. As an illustration, we applied SNPHunter for selecting SNPs for 10 major candidate genes for type 2 diabetes, including CAPN10, FABP4, IL6, NOS3, PPARG, TNF, UCP2, CRP, ESR1, and AR.

Conclusion

SNPHunter constitutes an efficient and user-friendly tool for SNP screening, selection, and acquisition. The executable and user's manual are available at http://www.hsph.harvard.edu/ppg/software.htm webcite.