THE ACCURACY OF DNA-SEQUENCES - ESTIMATING SEQUENCE QUALITY
THE ACCURACY OF DNA-SEQUENCES - ESTIMATING SEQUENCE QUALITY
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DOI：
10.1016/s0888-7543(05)80288-5
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发表时间：
1992-09-01
期刊：
影响因子：
4.4
通讯作者：
WATERMAN, MS
中科院分区：
文献类型：
--
作者：
CHURCHILL, GA;WATERMAN, MS
在本文中，我们描述了一个大的DNA序列从一组测序片段的统计重建的方法。我们假设片段已经被组装，并解决了确定重建序列没有错误的程度的问题，即，它的准确性。基于单个片段中的测序错误率，从组装的片段构型推导出共有分布。共有分布可用于找到满足预先指定的置信水平的最小冗余共有序列，无论是逐个碱基还是跨越序列的任何区域。描述了一种基于似然性的程序，用于估计测序错误率，该程序利用迭代EM算法。误差率的先验知识很容易被纳入估计过程。将所述方法应用于来自人G6PD基因座的一组组装的序列片段。在论文的最后，我们简要讨论了这项工作的相关性和实际意义。
In this paper we describe a method for the statistical reconstruction of a large DNA sequence from a set of sequenced fragments. We assume that the fragments have been assembled and address the problem of determining the degree to which the reconstructed sequence is free from errors, i.e., its accuracy. A consensus distribution is derived from the assembled fragment configuration based upon the rates of sequencing errors in the individual fragments. The consensus distribution can be used to find a minimally redundant consensus sequence that meets a prespecified confidence level, either base by base or across any region of the sequence. A likelihood-based procedure for the estimation of the sequencing error rates, which utilizes an iterative EM algorithm, is described. Prior knowledge of the error rates is easily incorporated into the estimation procedure. The methods are applied to a set of assembled sequence fragments from the human G6PD locus. We close the paper with a brief discussion of the relevance and practical implications of this work.