TY - GEN
T1 - Enumeration of RNA secondary structures
T2 - 40th Asilomar Conference on Signals, Systems, and Computers, ACSSC '06
AU - Milenkovic, Olgica
AU - Soljanin, Emina
PY - 2006
Y1 - 2006
N2 - 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.
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.
UR - http://www.scopus.com/inward/record.url?scp=47049120304&partnerID=8YFLogxK
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U2 - 10.1109/ACSSC.2006.355105
DO - 10.1109/ACSSC.2006.355105
M3 - Conference contribution
AN - SCOPUS:47049120304
SN - 1424407850
SN - 9781424407859
T3 - Conference Record - Asilomar Conference on Signals, Systems and Computers
SP - 1954
EP - 1958
BT - Conference Record of the 40th Asilomar Conference on Signals, Systems and Computers, ACSSC '06
Y2 - 29 October 2006 through 1 November 2006
ER -