Enumeration of RNA secondary structures: A constrained coding approach

Olgica Milenkovic, Emina Soljanin

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

Abstract

We consider the problem of enumerating and generating predefined RNA secondary structures in terms of classical constrained coding techniques and new grammarbased extensions thereof. First, we define a class of constraints, termed stem-loop constraints, that restrict the separation length of a phrase and its reverse-complement in both binary sequences and DNA/RNA sequences. For a simple subclass of this constraint, we evaluate the underlying channel capacity. Then we proceed to analyze stem-loop constraints for RNA secondary structures represented by context-free languages. The derived results provide a means for studying the shape diversity of pools of RNA strands involved in the process of aptamer design and identification.

Original languageEnglish (US)
Title of host publicationConference Record of the 40th Asilomar Conference on Signals, Systems and Computers, ACSSC '06
Pages1954-1958
Number of pages5
DOIs
StatePublished - 2006
Externally publishedYes
Event40th Asilomar Conference on Signals, Systems, and Computers, ACSSC '06 - Pacific Grove, CA, United States
Duration: Oct 29 2006Nov 1 2006

Publication series

NameConference Record - Asilomar Conference on Signals, Systems and Computers
ISSN (Print)1058-6393

Other

Other40th Asilomar Conference on Signals, Systems, and Computers, ACSSC '06
Country/TerritoryUnited States
CityPacific Grove, CA
Period10/29/0611/1/06

ASJC Scopus subject areas

  • Signal Processing
  • Computer Networks and Communications

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