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

Producción científica: Article › revisión exhaustiva

4 Citas (Scopus)

Resumen

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.

Idioma original	English (US)
Páginas (desde-hasta)	814-822
Número de páginas	9
Publicación	BioTechniques
Volumen	33
N.º	4
DOI	https://doi.org/10.2144/02334st05
Estado	Published - oct 1 2002
Publicado de forma externa	Sí

ASJC Scopus subject areas

General Biochemistry, Genetics and Molecular Biology
Biotechnology

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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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AU - Flood, Elizabeth M.

AU - Tang, F.

AU - Horvath, M. M.

AU - Pertsemlidis, A.

AU - Garner, H. R.

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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

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