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» Problems on RNA Secondary Structure Prediction and Design
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BMCBI
2004
151views more  BMCBI 2004»
13 years 8 months ago
Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics
Background: The general problem of RNA secondary structure prediction under the widely used thermodynamic model is known to be NP-complete when the structures considered include a...
Jens Reeder, Robert Giegerich
ASAP
2008
IEEE
186views Hardware» more  ASAP 2008»
14 years 3 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...
BMCBI
2007
153views more  BMCBI 2007»
13 years 8 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
2011
13 years 3 months ago
Multithreaded comparative RNA secondary structure prediction using stochastic context-free grammars
Background: The prediction of the structure of large RNAs remains a particular challenge in bioinformatics, due to the computational complexity and low levels of accuracy of state...
Zsuzsanna Sukosd, Bjarne Knudsen, Morten Vaerum, J...
BMCBI
2007
105views more  BMCBI 2007»
13 years 8 months ago
Predicting RNA secondary structure by the comparative approach: how to select the homologous sequences
Background: The secondary structure of an RNA must be known before the relationship between its structure and function can be determined. One way to predict the secondary structur...
Stefan Engelen, Fariza Tahi