Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints.

ABSTRACT:

Background

We are interested in the problem of predicting secondary structure for small sets of homologous RNAs, by incorporating limited comparative sequence information into an RNA folding model. The Sankoff algorithm for simultaneous RNA folding and alignment is a basis for approaches to this problem. There are two open problems in applying a Sankoff algorithm: development of a good unified scoring system for alignment and folding and development of practical heuristics for dealing with the computational complexity of the algorithm.

Results

We use probabilistic models (pair stochastic context-free grammars, pairSCFGs) as a unifying framework for scoring pairwise alignment and folding. A constrained version of the pairSCFG structural alignment algorithm was developed which

SUBMITTER: Dowell RD 

PROVIDER: S-EPMC1579236 | biostudies-literature | 2006 Sep

REPOSITORIES: biostudies-literature