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» RNA Pseudoknot Prediction Using Term Rewriting
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WABI
2007
Springer
13 years 11 months ago
HFold: RNA Pseudoknotted Secondary Structure Prediction Using Hierarchical Folding
Hosna Jabbari, Anne Condon, Ana Pop, Cristina Pop,...
BIBE
2007
IEEE
138views Bioinformatics» more  BIBE 2007»
13 years 11 months ago
A Flexible Stem-Based Local Search Algorithm for Predicting RNA Secondary Structures Including Pseudoknots
-We demonstrate a new algorithm named FlexStem to predict RNA secondary structures with pseudoknots. Our approach is based on the free energy minimization criterion, and utilizes a...
Xiang Chen, Simin He, Dongbo Bu, Runsheng Chen, We...
WABI
2007
Springer
133views Bioinformatics» more  WABI 2007»
13 years 11 months ago
RNA Folding Including Pseudoknots: A New Parameterized Algorithm and Improved Upper Bound
Predicting the secondary structure of an RNA sequence is an important problem in structural bioinformatics. The general RNA folding problem, where the sequence to be folded may con...
Chunmei Liu, Yinglei Song, Louis W. Shapiro
ISBRA
2007
Springer
13 years 11 months ago
Delta: A Toolset for the Structural Analysis of Biological Sequences on a 3D Triangular Lattice
Abstract. The lattice approach to biological structural analysis was made popular by the HP model for protein folding, but had not been used previously for RNA secondary structure ...
Minghui Jiang, Martin Mayne, Joel Gillespie
IPPS
2007
IEEE
13 years 11 months ago
RNAVLab: A unified environment for computational RNA structure analysis based on grid computing technology
Ribonucleic acid (RNA) molecules play important roles in many biological processes including gene expression and regulation. An RNA molecule is a linear polymer which folds back o...
Michela Taufer, Ming-Ying Leung, Kyle L. Johnson, ...