ArticleBMC bioinformatics2005
SNPHunter: a bioinformatic software for single nucleotide polymorphism data acquisition and management.
Article in BMC bioinformatics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Multivariate genome-wide association studies on tenderness of Berkshire and Duroc pig breeds.Genes & genomics · 2018Article
- snp-search: simple processing, manipulation and searching of SNPs from high-throughput sequencing.BMC bioinformatics · 2013Article
- A prospective study of leukocyte telomere length and risk of type 2 diabetes in postmenopausal women.Diabetes · 2012Article
- The human fatty acid-binding protein family: evolutionary divergences and functions.Human genomics · 2011Review
- Common genetic variants in fatty acid-binding protein-4 (FABP4) and clinical diabetes risk in the Women's Health Initiative Observational Study.Obesity (Silver Spring, Md.) · 2010Article
- Dynamic programming for single nucleotide polymorphism ID identification in systematic association studies.The Kaohsiung journal of medical sciences · 2009Article
- Relation of genetic variation in the gene coding for C-reactive protein with its plasma protein concentrations: findings from the Women's Health Initiative Observational Cohort.Clinical chemistry · 2009Article
- Interleukin and interleukin receptor gene polymorphisms and susceptibility to melanoma.Melanoma research · 2008Article
- Snagger: a user-friendly program for incorporating additional information for tagSNP selection.BMC bioinformatics · 2008Article
- SNPLims: a data management system for genome wide association studies.BMC bioinformatics · 2008Article
- A consolidated catalogue and graphical annotation of dbSNP polymorphisms in the human tissue kallikrein (KLK) locus.Molecular oncology · 2007Article
- QuickSNP: an automated web server for selection of tagSNPs.Nucleic acids research · 2007Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
backgroundSingle 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.
resultsWe 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.
conclusionSNPHunter 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
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