Enumeration of RNA secondary structures: A constrained coding approach

Olgica Milenkovic; Emina Soljanin

doi:10.1109/ACSSC.2006.355105

Enumeration of RNA secondary structures: A constrained coding approach

Research output: Chapter in Book/Report/Conference proceeding › Conference 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 language	English (US)
Title of host publication	Conference Record of the 40th Asilomar Conference on Signals, Systems and Computers, ACSSC '06
Pages	1954-1958
Number of pages	5
DOIs	https://doi.org/10.1109/ACSSC.2006.355105
State	Published - 2006
Externally published	Yes
Event	40th Asilomar Conference on Signals, Systems, and Computers, ACSSC '06 - Pacific Grove, CA, United States Duration: Oct 29 2006 → Nov 1 2006

Publication series

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

Other

Other	40th Asilomar Conference on Signals, Systems, and Computers, ACSSC '06
Country/Territory	United States
City	Pacific Grove, CA
Period	10/29/06 → 11/1/06

ASJC Scopus subject areas

Signal Processing
Computer Networks and Communications

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10.1109/ACSSC.2006.355105

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Enumeration of RNA secondary structures : A constrained coding approach. / Milenkovic, Olgica; Soljanin, Emina.

Conference Record of the 40th Asilomar Conference on Signals, Systems and Computers, ACSSC '06. 2006. p. 1954-1958 4176915 (Conference Record - Asilomar Conference on Signals, Systems and Computers).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Milenkovic, O & Soljanin, E 2006, Enumeration of RNA secondary structures: A constrained coding approach. in Conference Record of the 40th Asilomar Conference on Signals, Systems and Computers, ACSSC '06., 4176915, Conference Record - Asilomar Conference on Signals, Systems and Computers, pp. 1954-1958, 40th Asilomar Conference on Signals, Systems, and Computers, ACSSC '06, Pacific Grove, CA, United States, 10/29/06. https://doi.org/10.1109/ACSSC.2006.355105

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AB - 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.

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Enumeration of RNA secondary structures: A constrained coding approach

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