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BMCBI
2007
134views more  BMCBI 2007»
9 years 7 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 p...
Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathe...
BMCBI
2007
153views more  BMCBI 2007»
9 years 7 months ago
Can Clustal-style progressive pairwise alignment of multiple sequences be used in RNA secondary structure prediction?
Background: In ribonucleic acid (RNA) molecules whose function depends on their final, folded three-dimensional shape (such as those in ribosomes or spliceosome complexes), the se...
Amelia B. Bellamy-Royds, Marcel Turcotte
BMCBI
2005
162views more  BMCBI 2005»
9 years 7 months ago
Accelerated probabilistic inference of RNA structure evolution
Background: Pairwise stochastic context-free grammars (Pair SCFGs) are powerful tools for evolutionary analysis of RNA, including simultaneous RNA sequence alignment and secondary...
Ian Holmes
ICASSP
2008
IEEE
10 years 1 months ago
Probabilistic structural alignment of RNA sequences
We propose an algorithm for estimating the common secondary structure, alignment, and posterior base pairing probabilities for two RNA sequences. A deļ¬nition of structural align...
Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathe...
ICASSP
2007
IEEE
10 years 1 months ago
Toward Turbo Decoding of RNA Secondary Structure
We propose an iterative probabilistic algorithm for estimation of RNA secondary structure using sequence data from two homologous sequences. The method is intended to exploit inte...
Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathe...
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