Tree decomposition based fast search of RNA structures including pseudoknots in genomes

DMCA

Tree decomposition based fast search of RNA structures including pseudoknots in genomes (2005)

Cached

Download Links

Other Repositories/Bibliography

DBLP

by Yinglei Song , Russell Malmberg , Liming Cai , Chunmei Liu , Fangfang Pan

Venue:	In Proceedings of 2005 Computational System Bioinformatics Conference
Citations:	14 - 7 self

BibTeX

@INPROCEEDINGS{Song05treedecomposition,
    author = {Yinglei Song and Russell Malmberg and Liming Cai and Chunmei Liu and Fangfang Pan},
    title = {Tree decomposition based fast search of RNA structures including pseudoknots in genomes},
    booktitle = {In Proceedings of 2005 Computational System Bioinformatics Conference},
    year = {2005},
    pages = {223--234},
    publisher = {IEEE Computer Society}
}

OpenURL

Abstract

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 pseudo-knots). 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 small parameter, � and is the size of the profiled RNA structure. Experiments show that the application of the alignment algorithm to search in genomes yields the same search accuracy as methods based on a Covariance model with a significant reduction in computation time. In particular, very accurate searches

Keyphrases

tree decomposition rna structure rna secondary structure conformational graph computer program rna family structure model slight increase alignment algorithm novel rna structure stem loop covariance model isomorphic subgraph efficient algorithm important approach computational method small tree width small parameter accurate rna structuresequence alignment significant reduction optimal alignment modelling framework search accuracy conformation graph computation time profiled rna structure tree decomposition yield accurate search dynamic programming consensus structure non-coding rna

DMCA