SNPCEQer: detecting SNPs in sequences generated by the Beckman CEQ2000 DNA Analysis System |
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| Authors: | Flood E M Tang F Horvath M M Pertsemlidis A Garner H R |
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| Institution: | Eugene McDermott Center for Human Growth and Development, The University of Texas, Southwestern Medical Center, Dallas 75390-8591, USA. elizabeth.flood@utsouthwestern.edu |
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| Abstract: | SNPCEQer identifies and reports SNPs in sequences obtained from the Beckman CEQ2000 DNA Analysis System. SNPCEQer aligns sequences obtained using CEQ2000 heterozygote detection analysis and reports discrepancies between individual sequences and the consensus sequence it generates from this set as SNPs when the individual base calls have high-quality values. SNPCEQer reported comparable numbers of SNPs to the UNIX-based PolyPhred (148 vs. 165, respectively) in regions amplified from eight genes. A total of 21 different SNPs was discovered. Each gene region was analyzed in 96-306 samples. SNPCEQer was designed to operate from Windows NT, making SNP detection more accessible to users without UNIX systems. SNPCEQer is available free of charge at http://innovation.swmed.edu. |
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