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Inferring short tandem repeat variation from paired-end short reads.

机译:从配对末端的短读段推断短串联重复序列的变异。

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The advances of high-throughput sequencing offer an unprecedented opportunity to study genetic variation. This is challenged by the difficulty of resolving variant calls in repetitive DNA regions. We present a Bayesian method to estimate repeat-length variation from paired-end sequence read data. The method makes variant calls based on deviations in sequence fragment sizes, allowing the analysis of repeats at lengths of relevance to a range of phenotypes. We demonstrate the method's ability to detect and quantify changes in repeat lengths from short read genomic sequence data across genotypes. We use the method to estimate repeat variation among 12 strains of Arabidopsis thaliana and demonstrate experimentally that our method compares favourably against existing methods. Using this method, we have identified all repeats across the genome, which are likely to be polymorphic. In addition, our predicted polymorphic repeats also included the only known repeat expansion in A. thaliana, suggesting an ability to discover potential unstable repeats.
机译:高通量测序的进展为研究遗传变异提供了前所未有的机会。解决重复DNA区域中变体调用的难度对此提出了挑战。我们提出了一种贝叶斯方法来估计配对末端序列读取数据的重复长度变异。该方法基于序列片段大小的差异进行变异调用,从而可以分析与一系列表型相关长度的重复序列。我们证明了该方法能够检测和量化来自跨基因型的短读基因组序列数据的重复长度的变化。我们使用该方法估计12个拟南芥菌株之间的重复变异,并通过实验证明我们的方法与现有方法相比具有优势。使用这种方法,我们已经确定了整个基因组中的所有重复,这些重复可能是多态的。此外,我们预测的多态性重复序列还包括拟南芥中唯一已知的重复序列扩展,表明发现潜在的不稳定重复序列的能力。

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