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BMC Bioinformatics. 2008 Dec 12;9 Suppl 12:S9. doi: 10.1186/1471-2105-9-S12-S9.

VarDetect: a nucleotide sequence variation exploratory tool.

Author information

1
Genome Institute, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phaholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand. chumpol.nga@biotec.or.th

Abstract

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 samples; a total of 32 individual DNA samples. In this comparison of automatic SNP detection tools, VarDetect achieved the highest detection efficiency.

AVAILABILITY:

VarDetect is compatible with most major operating systems such as Microsoft Windows, Linux, and Mac OSX. The current version of VarDetect is freely available at http://www.biotec.or.th/GI/tools/vardetect.

PMID:
19091032
PMCID:
PMC2638149
DOI:
10.1186/1471-2105-9-S12-S9
[Indexed for MEDLINE]
Free PMC Article
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