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BMCBI
2008

VarDetect: a nucleotide sequence variation exploratory tool

9 years 1 months ago
VarDetect: a nucleotide sequence variation exploratory tool
Background: Single nucleotide polymorphisms (SNPs) are the most commonly studied units of genetic variation. The discovery of such variation may help to identify causative gene mutations in monogenic diseases and SNPs associated with predisposing genes in complex diseases. Accurate detection of SNPs requires software that can correctly interpret chromatogram signals to nucleotides. Results: We present VarDetect, a stand-alone nucleotide variation exploratory tool that automatically detects nucleotide variation from fluorescence based chromatogram traces. Accurate SNP base-calling is achieved using pre-calculated peak content ratios, and is enhanced by rules which account for common sequence reading artifacts. The proposed software tool is benchmarked against four other well-known SNP discovery software tools (PolyPhred, novoSNP, Genalys and Mutation Surveyor) using fluorescence based chromatograms from 15 human genes. These chromatograms were obtained from sequencing 16 two-pooled DNA...
Chumpol Ngamphiw, Supasak Kulawonganunchai, Anunch
Added 09 Dec 2010
Updated 09 Dec 2010
Type Journal
Year 2008
Where BMCBI
Authors Chumpol Ngamphiw, Supasak Kulawonganunchai, Anunchai Assawamakin, Ekachai Jenwitheesuk, Sissades Tongsima
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