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» RNA Secondary Structure Prediction with Simple Pseudoknots

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BIBE
2007
IEEE

138views Bioinformatics» more BIBE 2007»

A Flexible Stem-Based Local Search Algorithm for Predicting RNA Secondary Structures Including Pseudoknots

14 years 4 days ago

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-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...

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AAIM
2007
Springer

145views Algorithms» more AAIM 2007»

Improved Approximation Algorithms for Predicting RNA Secondary Structures with Arbitrary Pseudoknots

13 years 12 months ago

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We study three closely related problems motivated by the prediction of RNA secondary structures with arbitrary pseudoknots: the MAXIMUM BASE PAIR STACKINGS problem proposed by Ieon...

Minghui Jiang

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GCB
2004
Springer

139views Biometrics» more GCB 2004»

Conserved RNA Pseudoknots

13 years 11 months ago

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: Pseudoknots are essential for the functioning of many small RNA molecules. In addition, viral RNAs often exhibit pseudoknots that are required at various stages of the viral life...

C. Thurner, Ivo L. Hofacker, Peter F. Stadler

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WABI
2007
Springer

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HFold: RNA Pseudoknotted Secondary Structure Prediction Using Hierarchical Folding

13 years 12 months ago