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一个用于在DNA序列数据中识别类tRNA结构的程序。

A program for the identification of tRNA-like structures in DNA sequence data.

作者信息

Marvel C C

出版信息

Nucleic Acids Res. 1986 Jan 10;14(1):431-5. doi: 10.1093/nar/14.1.431.

DOI:10.1093/nar/14.1.431
PMID:3753778
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC339427/
Abstract

A computer algorithm has been developed which identifies tRNA genes and tRNA-like structures in DNA sequences. The program searches the sequence string for specific base positions that correspond to the invariant and semi-invariant bases found in tRNAs. The tRNA nature of the sequence is confirmed by the presence of complementary base pairing at the tRNA's calculated 5' and 3' ends (which in situ constitutes the amino-acyl stem region). The program achieves greater than 96% accuracy when run against known tRNA sequences in the Genbank database. The program is modular and is readily modified to allow searching either a file or database. The program is written in "C" and operates on a D.E.C. Vax 750. The utility of the algorithm is demonstrated by the identification of a distinctive tRNA structure in an intron of a published bovine hemoglobin gene.

摘要

已经开发出一种计算机算法，可识别DNA序列中的tRNA基因和tRNA样结构。该程序在序列字符串中搜索与tRNA中发现的不变和半不变碱基相对应的特定碱基位置。通过在tRNA计算出的5'和3'末端存在互补碱基配对（原位构成氨酰基茎区）来确认序列的tRNA性质。当针对Genbank数据库中的已知tRNA序列运行时，该程序的准确率超过96%。该程序是模块化的，很容易修改以允许搜索文件或数据库。该程序用“C”语言编写，在DEC Vax 750上运行。通过在已发表的牛血红蛋白基因的一个内含子中识别出一种独特的tRNA结构，证明了该算法的实用性。

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本文引用的文献

1
The leader mRNA of the histidine attenuator region resembles tRNAHis: possible general regulatory implications.组氨酸衰减子区域的前导mRNA类似于组氨酸转运RNA：可能具有普遍的调控意义。
Proc Natl Acad Sci U S A. 1983 Sep;80(17):5240-2. doi: 10.1073/pnas.80.17.5240.
2
Ruminant globin gene structures suggest an evolutionary role for Alu-type repeats.反刍动物珠蛋白基因结构表明Alu型重复序列具有进化作用。
Nucleic Acids Res. 1984 Feb 10;12(3):1641-55. doi: 10.1093/nar/12.3.1641.

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