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BMCBI
2007

Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign

9 years 6 months ago
Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign
Background: Joint alignment and secondary structure prediction of two RNA sequences can significantly improve the accuracy of the structural predictions. Methods addressing this problem, however, are forced to employ constraints that reduce computation by restricting the alignments and/or structures (i.e. folds) that are permissible. In this paper, a new methodology is presented for the purpose of establishing alignment constraints based on nucleotide alignment and insertion posterior probabilities. Using a hidden Markov model, posterior probabilities of alignment and insertion are computed for all possible pairings of nucleotide positions from the two sequences. These alignment and insertion posterior probabilities are additively combined to obtain probabilities of co-incidence for nucleotide position pairs. A suitable alignment constraint is obtained by thresholding the co-incidence probabilities. The constraint is integrated with Dynalign, a free energy minimization algorithm for j...
Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathe
Added 09 Dec 2010
Updated 09 Dec 2010
Type Journal
Year 2007
Where BMCBI
Authors Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathews
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