DNA evolutionary linguistics and RNA structure modeling: A computational approach

Takashi Yokomori, Satoshi Kobayashi

Research output: Chapter in Book/Report/Conference proceedingConference contribution

19 Citations (Scopus)

Abstract

In this paper, we are concerned with analyzing formal linguistic properties of DNA sequences in which a number of the language theoretic analysis on DNA sequences are established by means of computational methods. First, employing formal language theoretic framework, we consider a kind of an evolutionary problem of DNA sequences, asking (1) how DNA sequences were initially created and then evolved (grew up,) to be a language of certain complexity, and (2) what primitive constructs were minimally required for the process of evolution. In terms of formal linguistic concepts, we present several results that provide our view on these questions at a conceptual level. Based on the formal analysis on these biological questions, we then choose a certain type of tree generating grammars called Tree Adjunct Grammars (TAG) to attack the problem of modeling the secondary structure of RNA sequences. By proposing an extended model of TAGs, we demonstrate the usefulness of the grammars for modeling some typical RNA secondary structures including `pseudoknots', which suggests that TAG families as RNA grammars have a great potential for RNA secondary structure prediction.

Original languageEnglish
Title of host publicationProc Int IEEE Symp Intell Neural Biol Syst
PublisherIEEE
Pages38-45
Number of pages8
Publication statusPublished - 1995
Externally publishedYes
EventProceedings of the International IEEE Symposium on Intelligence in Neural and Biological Systems - Herndon, VA, USA
Duration: 1995 May 291995 May 31

Other

OtherProceedings of the International IEEE Symposium on Intelligence in Neural and Biological Systems
CityHerndon, VA, USA
Period95/5/2995/5/31

Fingerprint

DNA sequences
RNA
Linguistics
DNA
Formal languages
Computational methods

ASJC Scopus subject areas

  • Engineering(all)

Cite this

Yokomori, T., & Kobayashi, S. (1995). DNA evolutionary linguistics and RNA structure modeling: A computational approach. In Proc Int IEEE Symp Intell Neural Biol Syst (pp. 38-45). IEEE.

DNA evolutionary linguistics and RNA structure modeling : A computational approach. / Yokomori, Takashi; Kobayashi, Satoshi.

Proc Int IEEE Symp Intell Neural Biol Syst. IEEE, 1995. p. 38-45.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Yokomori, T & Kobayashi, S 1995, DNA evolutionary linguistics and RNA structure modeling: A computational approach. in Proc Int IEEE Symp Intell Neural Biol Syst. IEEE, pp. 38-45, Proceedings of the International IEEE Symposium on Intelligence in Neural and Biological Systems, Herndon, VA, USA, 95/5/29.
Yokomori T, Kobayashi S. DNA evolutionary linguistics and RNA structure modeling: A computational approach. In Proc Int IEEE Symp Intell Neural Biol Syst. IEEE. 1995. p. 38-45
Yokomori, Takashi ; Kobayashi, Satoshi. / DNA evolutionary linguistics and RNA structure modeling : A computational approach. Proc Int IEEE Symp Intell Neural Biol Syst. IEEE, 1995. pp. 38-45
@inproceedings{a12df5d1e5cd4f82ad5ee8cfc9735378,
title = "DNA evolutionary linguistics and RNA structure modeling: A computational approach",
abstract = "In this paper, we are concerned with analyzing formal linguistic properties of DNA sequences in which a number of the language theoretic analysis on DNA sequences are established by means of computational methods. First, employing formal language theoretic framework, we consider a kind of an evolutionary problem of DNA sequences, asking (1) how DNA sequences were initially created and then evolved (grew up,) to be a language of certain complexity, and (2) what primitive constructs were minimally required for the process of evolution. In terms of formal linguistic concepts, we present several results that provide our view on these questions at a conceptual level. Based on the formal analysis on these biological questions, we then choose a certain type of tree generating grammars called Tree Adjunct Grammars (TAG) to attack the problem of modeling the secondary structure of RNA sequences. By proposing an extended model of TAGs, we demonstrate the usefulness of the grammars for modeling some typical RNA secondary structures including `pseudoknots', which suggests that TAG families as RNA grammars have a great potential for RNA secondary structure prediction.",
author = "Takashi Yokomori and Satoshi Kobayashi",
year = "1995",
language = "English",
pages = "38--45",
booktitle = "Proc Int IEEE Symp Intell Neural Biol Syst",
publisher = "IEEE",

}

TY - GEN

T1 - DNA evolutionary linguistics and RNA structure modeling

T2 - A computational approach

AU - Yokomori, Takashi

AU - Kobayashi, Satoshi

PY - 1995

Y1 - 1995

N2 - In this paper, we are concerned with analyzing formal linguistic properties of DNA sequences in which a number of the language theoretic analysis on DNA sequences are established by means of computational methods. First, employing formal language theoretic framework, we consider a kind of an evolutionary problem of DNA sequences, asking (1) how DNA sequences were initially created and then evolved (grew up,) to be a language of certain complexity, and (2) what primitive constructs were minimally required for the process of evolution. In terms of formal linguistic concepts, we present several results that provide our view on these questions at a conceptual level. Based on the formal analysis on these biological questions, we then choose a certain type of tree generating grammars called Tree Adjunct Grammars (TAG) to attack the problem of modeling the secondary structure of RNA sequences. By proposing an extended model of TAGs, we demonstrate the usefulness of the grammars for modeling some typical RNA secondary structures including `pseudoknots', which suggests that TAG families as RNA grammars have a great potential for RNA secondary structure prediction.

AB - In this paper, we are concerned with analyzing formal linguistic properties of DNA sequences in which a number of the language theoretic analysis on DNA sequences are established by means of computational methods. First, employing formal language theoretic framework, we consider a kind of an evolutionary problem of DNA sequences, asking (1) how DNA sequences were initially created and then evolved (grew up,) to be a language of certain complexity, and (2) what primitive constructs were minimally required for the process of evolution. In terms of formal linguistic concepts, we present several results that provide our view on these questions at a conceptual level. Based on the formal analysis on these biological questions, we then choose a certain type of tree generating grammars called Tree Adjunct Grammars (TAG) to attack the problem of modeling the secondary structure of RNA sequences. By proposing an extended model of TAGs, we demonstrate the usefulness of the grammars for modeling some typical RNA secondary structures including `pseudoknots', which suggests that TAG families as RNA grammars have a great potential for RNA secondary structure prediction.

UR - http://www.scopus.com/inward/record.url?scp=0029210591&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0029210591&partnerID=8YFLogxK

M3 - Conference contribution

AN - SCOPUS:0029210591

SP - 38

EP - 45

BT - Proc Int IEEE Symp Intell Neural Biol Syst

PB - IEEE

ER -