IDENTIFICATION OF NEW EUKARYOTIC TRANSFER-RNA GENES IN GENOMIC DNA DATABASES BY A MULTISTEP WEIGHT MATRIX ANALYSIS OF TRANSCRIPTIONAL CONTROL REGIONS
IDENTIFICATION OF NEW EUKARYOTIC TRANSFER-RNA GENES IN GENOMIC DNA DATABASES BY A MULTISTEP WEIGHT MATRIX ANALYSIS OF TRANSCRIPTIONAL CONTROL REGIONS
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DOI：
10.1093/nar/22.7.1247
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发表时间：
1994-04-11
影响因子：
14.9
通讯作者：
OTTONELLO, S
中科院分区：
文献类型：
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作者：
PAVESI, A;CONTERIO, F;OTTONELLO, S
描述了在 DNA 数据库中搜索真核核 tRNA 基因的线性方法。基于一般权重矩阵程序的修改版本，我们的算法依赖于对称为 A 和 B 盒的两个基因内控制区域的识别、转录终止信号以及对这些元件之间的间距的评估。使用该搜索算法扫描真核细胞核 DNA 数据库，正确识别了 940 个已知 tRNA 基因中的 933 个（假阴性的 0.74%）。鉴定出 30 个新的潜在 tRNA 基因，其中两个基因的转录活性通过体外转录直接得到验证。该算法的总误报率为0.014%。结构上不寻常的 tRNA 基因，如编码硒代半胱氨酸 tRNA 的基因，也可以使用一组有关其特定特性的规则来识别，并且编码此类 tRNA 的一个人类基因已被识别。一些新发现的 tRNA 基因被发现位于相当不常见的基因组位置：2 个位于着丝粒区域，3 个位于内含子内。此外，可以通过标准搜索程序的特定子程序检测来自不同生物体的 tRNA 基因中是否存在基因外 B 盒。
A linear method for the search of eukaryotic nuclear tRNA genes in DNA databases is described. Based on a modified version of the general weight matrix procedure, our algorithm relies on the recognition of two intragenic control regions known as A and B boxes, a transcription termination signal, and on the evaluation of the spacing between these elements. The scanning of the eukaryotic nuclear DNA database using this search algorithm correctly identified 933 of the 940 known tRNA genes (0.74% of false negatives). Thirty new potential tRNA genes were identified, and the transcriptional activity of two of them was directly verified by in vitro transcription. The total false positive rate of the algorithm was 0.014%. Structurally unusual tRNA genes, like those coding for selenocysteine tRNAs, could also be recognized using a set of rules concerning their specific properties, and one human gene coding for such tRNA was identified. Some of the newly identified tRNA genes were found in rather uncommon genomic positions: 2 in centromeric regions and 3 within introns. Furthermore, the presence of extragenically located B boxes in tRNA genes from various organisms could be detected through a specific subroutine of the standard search program.