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» RNA Secondary Structure Prediction with Simple Pseudoknots
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BMCBI
2004
116views more  BMCBI 2004»
13 years 7 months ago
Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure p
Background: A detailed understanding of an RNA's correct secondary and tertiary structure is crucial to understanding its function and mechanism in the cell. Free energy mini...
Kishore J. Doshi, Jamie J. Cannone, Christian W. C...
METMBS
2004
196views Mathematics» more  METMBS 2004»
13 years 8 months ago
An Open Problem in RNA Secondary Structure Prediction by the Comparative Approach
Abstract One approach to predict the secondary structure of RNA is the comparative approach. This approach is used when alignment of several homologous sequences of a RNA is availa...
Stefan Engelen, Fariza Tahi
ICASSP
2008
IEEE
14 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 definition of structural align...
Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathe...
SAC
2009
ACM
14 years 2 months ago
GTfold: a scalable multicore code for RNA secondary structure prediction
The prediction of the correct secondary structures of large RNAs is one of the unsolved challenges of computational molecular biology. Among the major obstacles is the fact that a...
Amrita Mathuriya, David A. Bader, Christine E. Hei...
ASAP
2008
IEEE
186views Hardware» more  ASAP 2008»
14 years 1 months ago
Accelerating Nussinov RNA secondary structure prediction with systolic arrays on FPGAs
RNA structure prediction, or folding, is a computeintensive task that lies at the core of several search applications in bioinformatics. We begin to address the need for high-thro...
Arpith C. Jacob, Jeremy Buhler, Roger D. Chamberla...