SNPCEQer: Detecting SNPs in sequences generated by the Beckman CEQ™2000 DNA Analysis System

Elizabeth M. Flood; F. Tang; M. M. Horvath; A. Pertsemlidis; H. R. Garner

doi:10.2144/02334st05

SNPCEQer: Detecting SNPs in sequences generated by the Beckman CEQ™2000 DNA Analysis System

Elizabeth M. Flood, F. Tang, M. M. Horvath, A. Pertsemlidis, H. R. Garner

Research output: Contribution to journal › Article › peer-review

4 Scopus citations

Abstract

SNPCEQer identifies and reports SNPs in sequences obtained from the Beckman CEQ™2000 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.

Original language	English (US)
Pages (from-to)	814-822
Number of pages	9
Journal	BioTechniques
Volume	33
Issue number	4
DOIs	https://doi.org/10.2144/02334st05
State	Published - Oct 1 2002
Externally published	Yes

ASJC Scopus subject areas

General Biochemistry, Genetics and Molecular Biology
Biotechnology

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title = "SNPCEQer: Detecting SNPs in sequences generated by the Beckman CEQ{\texttrademark}2000 DNA Analysis System",

abstract = "SNPCEQer identifies and reports SNPs in sequences obtained from the Beckman CEQ{\texttrademark}2000 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{\textregistered}, 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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T1 - SNPCEQer

T2 - Detecting SNPs in sequences generated by the Beckman CEQ™2000 DNA Analysis System

AU - Flood, Elizabeth M.

AU - Tang, F.

AU - Horvath, M. M.

AU - Pertsemlidis, A.

AU - Garner, H. R.

PY - 2002/10/1

Y1 - 2002/10/1

N2 - SNPCEQer identifies and reports SNPs in sequences obtained from the Beckman CEQ™2000 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.

AB - SNPCEQer identifies and reports SNPs in sequences obtained from the Beckman CEQ™2000 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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SNPCEQer: Detecting SNPs in sequences generated by the Beckman CEQ™2000 DNA Analysis System

Abstract

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