DNA序列中蛋白质编码区域的识别。
Recognition of protein coding regions in DNA sequences.
作者信息
Fickett J W
出版信息
Nucleic Acids Res. 1982 Sep 11;10(17):5303-18. doi: 10.1093/nar/10.17.5303.
Abstract
We give a test for protein coding regions which is based on simple and universal differences between protein-coding and noncoding DNA. The test is simple enough to use without a computer and is completely objective. The test has been thoroughly proven on 400,000 bases of sequence data: it misclassifies 5% of the regions tested and gives an answer of "No Opinion" one fifth of the time. We predict some new coding and noncoding regions in published sequences.
摘要
我们给出了一种针对蛋白质编码区域的检测方法，该方法基于蛋白质编码DNA和非编码DNA之间简单且通用的差异。该检测方法简单到无需计算机即可使用，而且完全客观。该检测方法已在40万个碱基的序列数据上得到充分验证：它对5%的测试区域分类错误，并且有五分之一的概率给出“无法判断”的结果。我们预测了已发表序列中的一些新的编码和非编码区域。
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本文引用的文献
1
Complete nucleotide sequence of the human delta-globin gene.人类δ-珠蛋白基因的完整核苷酸序列。
Cell. 1980 Oct;21(3):639-46. doi: 10.1016/0092-8674(80)90427-4.
2
Transfer-RNA, an early gene?转运核糖核酸，一种早期基因？
Naturwissenschaften. 1981 Jun;68(6):282-92. doi: 10.1007/BF01047470.
3
Periodic correlations in DNA sequences and evidence suggesting their evolutionary origin in a comma-less genetic code.DNA序列中的周期性相关性以及表明其在无逗号遗传密码中进化起源的证据。
J Mol Evol. 1981;17(2):94-102. doi: 10.1007/BF01732679.
4
Codon catalog usage is a genome strategy modulated for gene expressivity.密码子编目使用是一种为基因表达性而调节的基因组策略。
Nucleic Acids Res. 1981 Jan 10;9(1):r43-74. doi: 10.1093/nar/9.1.213-b.
5
Lysis gene expression of RNA phage MS2 depends on a frameshift during translation of the overlapping coat protein gene.RNA噬菌体MS2的裂解基因表达取决于重叠衣壳蛋白基因翻译过程中的移码。
Nature. 1982 Jan 7;295(5844):35-41. doi: 10.1038/295035a0.
6
Codon preference and its use in identifying protein coding regions in long DNA sequences.密码子偏好性及其在长DNA序列中识别蛋白质编码区的应用。
Nucleic Acids Res. 1982 Jan 11;10(1):141-56. doi: 10.1093/nar/10.1.141.
7
Key for protein coding sequences identification: computer analysis of codon strategy.蛋白质编码序列识别的关键：密码子策略的计算机分析
Nucleic Acids Res. 1982 Jan 11;10(1):391-402. doi: 10.1093/nar/10.1.391.
8
The mosaic organization of the apocytochrome b gene of Aspergillus nidulans revealed by DNA sequencing.通过DNA测序揭示的构巢曲霉脱辅基细胞色素b基因的镶嵌组织。
Cell. 1981 Nov;27(1 Pt 2):4-11. doi: 10.1016/0092-8674(81)90354-8.
9
Promoters in the E. coli replication origin.大肠杆菌复制起点中的启动子。
Nature. 1981 Nov 26;294(5839):376-8. doi: 10.1038/294376a0.
10
Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli.大肠杆菌核糖体RNA操纵子的基因组织与一级结构
J Mol Biol. 1981 May 15;148(2):107-27. doi: 10.1016/0022-2836(81)90508-8.
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