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Bioinformatics Advance Access published online on September 17, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth486
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received February 7, 2004
Revised July 27, 2004
Accepted August 13, 2004

Applications note

SNPP: automating large-scale SNP genotype data management

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

1 Laboratory of Molecular and Statistical Genetics, College of Life Sciences Hunan Normal University, Changsha, Hunan 410081, P. R. China; Department of Biomedical Sciences, Creighton University, Omaha, NE 68131, USA; Osteoporosis Research Center, Creighton University Medical Center Omaha, NE 68131, USA
2 Laboratory of Molecular and Statistical Genetics, College of Life Sciences Hunan Normal University, Changsha, Hunan 410081, P. R. China
3 Department of Biomedical Sciences, Creighton University, Omaha, NE 68131, USA; Osteoporosis Research Center, Creighton University Medical Center Omaha, NE 68131, USA
4 Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06516, USA
5 Laboratory of Molecular and Statistical Genetics, College of Life Sciences Hunan Normal University, Changsha, Hunan 410081, P. R. China; 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, P.R.China; Department of Biomedical Sciences, Creighton University, Omaha, NE 68131, USA; Osteoporosis Research Center, Creighton University Medical Center Omaha, NE 68131, USA

* To whom correspondence should be addressed. E-mail: deng{at}creighton.edu.


  Abstract

Summary: To manage high-throughput 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/.


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