Tree Decomposition Based Fast Search of RNA Structures Including Pseudoknots in Genomes

Searching genomes for RNA secondary structure with computational methods has become an important approach to the annotation of non-coding RNAs. However, due to the lack of efficient algorithms for accurate RNA structuresequence alignment, computer programs capable of fast and effectively searching genomes for RNA secondary structures have not been available. In this paper, a novel RNA structure profiling model is introduced based on the notion of a conformational graph to specify the consensus structure of an RNA family. Tree decomposition yields a small tree width   for such conformation graphs (e.g.,  ¢¡¤£ for stem loops and only a slight increase for pseudoknots). Within this modelling framework, the optimal alignment of a sequence to the structure model corresponds to finding a maximum valued isomorphic subgraph and consequently can be accomplished through dynamic programming on the tree decomposition of the conformational graph in time ¥§¦©¨ , where ¨ is a ...

• Type: Conference
• Year: 2005
• Where: CSB
• Authors: Yinglei Song, Chunmei Liu, Russell L. Malmberg, Fangfang Pan, Liming Cai
• Keywords: Bioinformatics, CSB 2005, Genomes, RNA Secondary Structures, Tree Decomposition