Enumerating RNA Motifs: A coding-Theoretic approach

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

Abstract

We consider the problem of enumerating RNA secondary structures that obey a set of structural constraints arising due to the bio-chemical properties of the sugar-phosphate backbone of the strands. The enumeration problem is cast into a framework involving context-free attribute grammars, where the grammars are used to obtain a closed-form expression for the q-generating functions of the constrained objects via the Delest-Fédou "attribute grammar" method. This approach can be viewed as an extension of the paradigm of constrained coding, which was so far used to operates on constraints represented by regular, rather than context-free languages.

Original languageEnglish (US)
Title of host publication44th Annual Allerton Conference on Communication, Control, and Computing 2006
PublisherUniversity of Illinois at Urbana-Champaign, Coordinated Science Laboratory and Department of Computer and Electrical Engineering
Pages492-501
Number of pages10
ISBN (Electronic)9781604237924
StatePublished - 2006
Externally publishedYes
Event44th Annual Allerton Conference on Communication, Control, and Computing 2006 - Monticello, United States
Duration: Sep 27 2006Sep 29 2006

Publication series

Name44th Annual Allerton Conference on Communication, Control, and Computing 2006
Volume1

Other

Other44th Annual Allerton Conference on Communication, Control, and Computing 2006
Country/TerritoryUnited States
CityMonticello
Period9/27/069/29/06

ASJC Scopus subject areas

  • Computer Science Applications
  • Computer Networks and Communications

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