Vacic Vladimir, Jin Hailing, Zhu Jian-Kang, Lonardi Stefano
Computer Science and Engineering Department, University of California, Riverside, USA.
Pac Symp Biocomput. 2008:75-86.
The 454 pyrosequencing technology is gaining popularity as an alternative to traditional Sanger sequencing. While each method has comparative advantages over the other, certain properties of the 454 method make it particularly well suited for small RNA discovery. We here describe some of the details of the 454 sequencing technique, with an emphasis on the nature of the intrinsic sequencing errors and methods for mitigating their effect. We propose a probabilistic framework for small RNA discovery, based on matching 454 flowgrams against the target genome. We formulate flowgram matching as an analog of profile matching, and adapt several profile matching techniques for the task of matching flowgrams. As a result, we are able to recover some of the hits missed by existing methods and assign probability-based scores to them.
454焦磷酸测序技术作为传统桑格测序的替代方法正越来越受欢迎。虽然每种方法都有相对其他方法的比较优势，但454方法的某些特性使其特别适合于小RNA的发现。我们在此描述454测序技术的一些细节，重点是内在测序错误的性质以及减轻其影响的方法。我们基于将454测序峰图与目标基因组进行匹配，提出了一个用于小RNA发现的概率框架。我们将测序峰图匹配表述为轮廓匹配的类似物，并采用几种轮廓匹配技术来完成测序峰图的匹配任务。结果，我们能够找回一些现有方法遗漏的匹配，并为它们赋予基于概率的分数。
