A probabilistic method for small RNA flowgram matching.
A probabilistic method for small RNA flowgram matching.
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DOI：
10.1142/9789812776136_0009
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发表时间：
2007-12
影响因子：
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通讯作者：
V. Vacic;Hailing Jin;Jian‐Kang Zhu;S. Lonardi
中科院分区：
文献类型：
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作者：
V. Vacic;Hailing Jin;Jian‐Kang Zhu;S. Lonardi
454焦磷酸测序技术作为传统Sanger测序的替代方案越来越受欢迎。虽然每种方法都具有相对优势，但454方法的某些特性使其特别适合小RNA的发现。我们在这里描述了454测序技术的一些细节，重点是固有测序误差的性质和减轻其影响的方法。我们提出了一个小RNA发现的概率框架，基于匹配454流程图与目标基因组。我们将流图匹配作为剖面匹配的类比，并采用了几种剖面匹配技术来完成流图匹配的任务。因此，我们能够恢复现有方法错过的一些命中，并为它们分配基于概率的分数。
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.