Detecting and analyzing DNA sequencing errors:: Toward a higher quality of the Bacillus subtilis genome sequence
Detecting and analyzing DNA sequencing errors:: Toward a higher quality of the Bacillus subtilis genome sequence
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DOI：
10.1101/gr.9.11.1116
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发表时间：
1999-11-01
期刊：
影响因子：
7
通讯作者：
Danchin, A
中科院分区：
文献类型：
--
作者：
Médigue, C;Rose, M;Danchin, A
在确定DNA序列的过程中，在推定基因中引入人为移码和/或框内终止密码子可导致基因产物的错误预测。只有当相关序列在数据库中可用时，才有可能用基于蛋白质相似性匹配的方法检测这种错误。Hele，我们提出了一种基于编码序列的内在动力的DNA序列移码错误检测方法。它结合了两种分析的结果，即翻译起始/终止位点的搜索和编码区的预测。该方法用于筛选枯草芽孢杆菌全基因组序列，并对推定错误的侧翼区域进行重新测序以进行验证。这个过程使我们能够纠正序列，并详细分析错误的性质。有趣的是，在一些情况下，火焰终止密码子或移码不是测序错误，但被证实存在于染色体中，表明这些基因要么是无功能的[假基因]，要么受到调控过程的影响，如程序化的翻译移码。该方法可用于检查任何原核基因组测序计划产生的序列的质量。
During the determination of a DNA sequence, the introduction of artifactual frameshifts and/or in-frame stop codons in putative genes can lead to misprediction of gene products. Detection of such errors with a methods based on protein similarity matching is only possible when related sequences are available in databases. Hele, we present a method to detect frameshift errors in DNA sequences that is based on the intrinsic propel ties of the coding sequences. It combines the results of two analyses, the search for translational initiation/termination sites and the prediction of coding regions. This method was used to screen the complete Bacillus subtilis genome sequence and the regions flanking putative errors were resequenced for verification. This procedure allowed us to correct the sequence and to analyze in detail the nature of the errors. Interestingly, in several cases in-flame termination codons or frameshifts were not sequencing errors but confirmed to be present in the chromosome, indicating that the genes are either nonfunctional [pseudogenes] or subject to regulatory processes such as programmed translational frameshifts. The method can be used for checking the quality of the sequences produced by any prokaryotic genome sequencing project.