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Bioinformatics Advance Access originally published online on September 17, 2004
Bioinformatics 2005 21(2):266-268; doi:10.1093/bioinformatics/bth486
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Bioinformatics vol. 21 issue 2 © Oxford University Press 2005; all rights reserved.

SNPP: automating large-scale SNP genotype data management

Lan-Juan Zhao 1,3,4,{dagger}, Miao-Xin Li 1,{dagger}, Yan-Fang Guo 1, Fu-Hua Xu 3,4, Jin-Long Li 5 and Hong-Wen Deng 1,2,3,4,*

1 Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University Changsha, Hunan 410081, China
2 The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University Xi'an 710049, China
3 Department of Biomedical Sciences, Creighton University Omaha, NE 68131, USA
4 Osteoporosis Research Center, Creighton University Medical Center Omaha, NE 68131, USA
5 Department of Psychiatry, Yale University School of Medicine New Haven, CT 06516, USA

*To whom correspondence should be addressed at Osteoporosis Research Center, Creighton University Medical Center, 601 N. 30th St. Suite 6787, Omaha, NE 68131, USA.

Summary: To manage high-throughput single nucleotide polymorphism (SNP) genotyping data efficiently, we developed a dynamic general database management system—SNPP (SNP Processor). It provides several functions, including data importing with comparison, Mendelian inheritance check within pedigrees, data compiling and exporting. Furthermore, SNPP may generate files for repeat genotyping and transform them into files that can be executed by a liquid handling system.

Availability: http://orclinux.creighton.edu/snpp/

Contact: lanjuanzhao{at}creighton.edu


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