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 journalArticle

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 languageEnglish (US)
Pages (from-to)814-822
Number of pages9
JournalBioTechniques
Volume33
Issue number4
DOIs
StatePublished - Oct 1 2002
Externally publishedYes

ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry, Genetics and Molecular Biology(all)

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