Canonical RNA Pseudoknot Structures

In this paper, we study k-noncrossing, -canonical RNA pseudoknot structures with minimum arc-length greater or equal to four. Let T OE4 k; .n/ denote the number of these structures. We derive exact enumeration results by computing the generating function TOE4 k; .z/ D P n T OE4 k; .n/zn and derive the asymptotic formulas T OE4 k;3 .n/ ck n .k 1/2 k 1 2 . OE4 k;3 / n for k D 3; : : :; 9. In particular, we have for k D 3, T OE4 3;3 .n/ c3 n 5 2:0348n . Our results show that the set of biophysically relevant RNA pseudoknot structures is surprisingly small and suggest a new structure class as target for prediction algorithms. Key words: canonical, enumeration, generating function, pseudoknot, RNA secondary structure, singularity analysis.

• Type: Journal
• Year: 2008
• Where: JCB
• Authors: Gang Ma, Christian M. Reidys
• Keywords: -canonical Rna Pseudoknot, JCB 2008, Minimum Arc-length, RNA Pseudoknot