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22

BIBE
2007
IEEE

138views Bioinformatics» more BIBE 2007»

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

14 years 1 months ago

-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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22

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CSB
2005
IEEE

114views Bioinformatics» more CSB 2005»

Tree Decomposition Based Fast Search of RNA Structures Including Pseudoknots in Genomes

14 years 1 months ago

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Searching genomes for RNA secondary structure with computational methods has become an important approach to the annotation of non-coding RNAs. However, due to the lack of efﬁci...

Yinglei Song, Chunmei Liu, Russell L. Malmberg, Fa...

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26

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AAIM
2007
Springer

145views Algorithms» more AAIM 2007»

Improved Approximation Algorithms for Predicting RNA Secondary Structures with Arbitrary Pseudoknots

14 years 1 months ago

Download digital.cs.usu.edu

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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24

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ISMB
1997

164views Computational Biology» more ISMB 1997»

Automated Alignment of RNA Sequences to Pseudoknotted Structures

13 years 9 months ago

Download www.aaai.org

Seq7 is a newprogramfor generating multiple structure-based alignments of RNAsequences. Byusing a variant of Dijkstra’s algorithm to find the shortest path through a specially c...

Jack E. Tabaska, Gary D. Stormo

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19

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WABI
2007
Springer

99views Bioinformatics» more WABI 2007»

HFold: RNA Pseudoknotted Secondary Structure Prediction Using Hierarchical Folding

14 years 1 months ago