Doi K, Imai H
Department of Information Science, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
Genome Inform Ser Workshop Genome Inform. 2000;11:53-62.
DNA sequencing is a very important problem in genomics. Several different sequencing methods are currently utilized. One promising method uses a sequencing chip to obtain information about the presence of subsequences in DNA. This paper deals with sequencing of hybridization data from a sequencing chip, called Sequencing by Hybridization (SBH). Preparata et al. proposed a new sequencing chip using universal bases, together with a new sequencing algorithm, and showed that its performance is significantly better than the standard scheme based on oligomer probes. However, the presence of errors in the sequencing chip was not considered, and the method of Preparata et al. cannot be used directly in practice. This paper proposes sequencing algorithms in the presence of hybridization errors for their sequencing chip and applies these algorithms to random data in the presence of random errors. Computational results show that false negative errors have larger effects on the rates of correct reconstruction than do false positive errors. Our extended sequencing algorithms are useful when there are a few hybridization errors.
DNA测序是基因组学中一个非常重要的问题。目前使用了几种不同的测序方法。一种有前景的方法是使用测序芯片来获取有关DNA中 subsequences 存在情况的信息。本文讨论来自一种称为杂交测序（SBH）的测序芯片的杂交数据的测序。Preparata等人提出了一种使用通用碱基的新型测序芯片以及一种新的测序算法，并表明其性能明显优于基于寡聚物探针的标准方案。然而，未考虑测序芯片中错误的存在，Preparata等人的方法在实际中不能直接使用。本文针对他们的测序芯片提出了存在杂交错误时的测序算法，并将这些算法应用于存在随机错误的随机数据。计算结果表明，假阴性错误对正确重建率的影响比假阳性错误更大。当存在一些杂交错误时，我们扩展的测序算法很有用。
