Literature DB >> 6200832

Genome structure described by formal languages.

V Brendel, H G Busse.   

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.

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Year:  1984        PMID： 6200832      PMCID： PMC318685          DOI： 10.1093/nar/12.5.2561

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  11 in total

1.  A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase.

Authors:  F Sanger; A R Coulson
Journal:  J Mol Biol       Date:  1975-05-25       Impact factor: 5.469

Review 2.  RNA processing and the intervening sequence problem.

Authors:  J Abelson
Journal:  Annu Rev Biochem       Date:  1979       Impact factor: 23.643

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Authors:  B Shapiro
Journal:  Comput Programs Biomed       Date:  1977-06

4.  A new method for sequencing DNA.

Authors:  A M Maxam; W Gilbert
Journal:  Proc Natl Acad Sci U S A       Date:  1977-02       Impact factor: 11.205

Review 5.  Initiation mechanisms of protein syntehesis.

Authors:  M Grunberg-Manago; F Gros
Journal:  Prog Nucleic Acid Res Mol Biol       Date:  1977

Review 6.  Structure and function of phage RNA.

Authors:  C Weissmann; M A Billeter; H M Goodman; J Hindley; H Weber
Journal:  Annu Rev Biochem       Date:  1973       Impact factor: 23.643

7.  Developmental systems without cellular interactions, their languages and grammars.

Authors:  A Lindenmayer
Journal:  J Theor Biol       Date:  1971-03       Impact factor: 2.691

8.  An automaton analogue of unicellularity.

Authors:  H M Martinez
Journal:  Biosystems       Date:  1979-08       Impact factor: 1.973

9.  The genetic code. 3.

Authors:  F H Crick
Journal:  Sci Am       Date:  1966-10       Impact factor: 2.142

10.  The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites.

Authors:  J Shine; L Dalgarno
Journal:  Proc Natl Acad Sci U S A       Date:  1974-04       Impact factor: 11.205
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  8 in total

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2.  Formal language theory and DNA: an analysis of the generative capacity of specific recombinant behaviors.

Authors:  T Head
Journal:  Bull Math Biol       Date:  1987       Impact factor: 1.758

3.  Information theoretic perspective on genome clustering.

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Journal:  Entropy (Basel)       Date:  2010-01-01       Impact factor: 2.524

5.  Compression principle and Zipf's Law of brevity in infochemical communication.

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6.  Different clustering of genomes across life using the A-T-C-G and degenerate R-Y alphabets: early and late signaling on genome evolution?

Authors:  V Kirzhner; A Paz; Z Volkovich; E Nevo; A Korol
Journal:  J Mol Evol       Date:  2007-03-19       Impact factor: 2.395

7.  A formal language-based approach in biology.

Authors:  Marian Gheorghe; Victor Mitrana
Journal:  Comp Funct Genomics       Date:  2004

8.  A stochastic context free grammar based framework for analysis of protein sequences.

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Journal:  BMC Bioinformatics       Date:  2009-10-08       Impact factor: 3.169
  8 in total

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