用形式语言描述的基因组结构。
Genome structure described by formal languages.
作者信息
Brendel V, Busse H G
出版信息
Nucleic Acids Res. 1984 Mar 12;12(5):2561-8. doi: 10.1093/nar/12.5.2561.
Abstract
Nucleic acid sequences may be looked upon as words over the alphabet of nucleotides. Naturally occurring DNAs and RNAs form subsets of the set of all possible words. The use of formal languages is proposed to describe the structure of these subsets. Regular languages defined by finite automata are introduced to demonstrate the application of the concept on RNA-phages of group I. This approach permits a concise characterization of grammatical patterns in genetic information.
摘要
核酸序列可以被看作是由核苷酸组成的字母表上的单词。天然存在的DNA和RNA构成了所有可能单词集合的子集。有人提议使用形式语言来描述这些子集的结构。引入由有限自动机定义的正则语言，以展示该概念在第一组RNA噬菌体中的应用。这种方法允许对遗传信息中的语法模式进行简洁的表征。
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本文引用的文献
1
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.
2
The genetic code. 3.遗传密码。3.
Sci Am. 1966 Oct;215(4):55-60 passim. doi: 10.1038/scientificamerican1066-55.
3
Developmental systems without cellular interactions, their languages and grammars.没有细胞相互作用的发育系统、它们的语言和语法。
J Theor Biol. 1971 Mar;30(3):455-84. doi: 10.1016/0022-5193(71)90002-6.
4
The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites.大肠杆菌16S核糖体RNA的3'末端序列：与无义三联体及核糖体结合位点的互补性
Proc Natl Acad Sci U S A. 1974 Apr;71(4):1342-6. doi: 10.1073/pnas.71.4.1342.
5
Structure and function of phage RNA.噬菌体RNA的结构与功能。
Annu Rev Biochem. 1973;42:303-28. doi: 10.1146/annurev.bi.42.070173.001511.
6
A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase.一种通过DNA聚合酶引发合成来测定DNA序列的快速方法。
J Mol Biol. 1975 May 25;94(3):441-8. doi: 10.1016/0022-2836(75)90213-2.
7
Language processor generation with BNF inputs: methods and implementation.
Comput Programs Biomed. 1977 Jun;7(2):85-98. doi: 10.1016/0010-468x(77)90015-0.
8
An automaton analogue of unicellularity.单细胞性的自动机类似物。
Biosystems. 1979 Aug;11(2-3):133-62. doi: 10.1016/0303-2647(79)90007-8.
9
Initiation mechanisms of protein syntehesis.蛋白质合成的起始机制。
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10
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