VarDetect: a nucleotide sequence variation exploratory tool.
VarDetect: a nucleotide sequence variation exploratory tool.
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DOI：
10.1186/1471-2105-9-s12-s9
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发表时间：
2008-12-12
影响因子：
3
通讯作者：
Tongsima S
中科院分区：
文献类型：
--
作者：
Ngamphiw C;Kulawonganunchai S;Assawamakin A;Jenwitheesuk E;Tongsima S
单核苷酸多态性（SNPs）是最常被研究的遗传变异单位。这种变异的发现可能有助于确定单基因疾病的致病基因突变和复杂疾病中与易感基因相关的snp。snp的准确检测需要软件能够正确地将色谱信号解释为核苷酸。我们提出VarDetect，一个独立的核苷酸变异探索工具，自动检测核苷酸变异从荧光为基础的色谱痕迹。准确的SNP碱基调用使用预先计算的峰值含量比来实现，并通过考虑常见序列读取伪影的规则来增强。所提出的软件工具与其他四个知名的SNP发现软件工具（PolyPhred, novoSNP， Genalys和Mutation Surveyor）进行了基准测试，使用基于荧光的15个人类基因色谱图。这些色谱图是从16个双池DNA样本测序得到的；总共32个DNA样本。在这个自动SNP检测工具的比较中，VarDetect的检测效率最高。VarDetect兼容大多数主流操作系统，如Microsoft Windows、Linux和Mac OSX。当前版本的VarDetect可以在。
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. 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. 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 .