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Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics.

Reeder J, Giegerich R.

BMC Bioinformatics. 2004 Aug 4;5:104.PMID: 15294028 [PubMed - indexed for MEDLINE]Related articlesFree article

A dynamic programming algorithm for RNA structure prediction including pseudoknots.

Rivas E, Eddy SR.

J Mol Biol. 1999 Feb 5;285(5):2053-68.PMID: 9925784 [PubMed - indexed for MEDLINE]Related articles

HotKnots: heuristic prediction of RNA secondary structures including pseudoknots.

Ren J, Rastegari B, Condon A, Hoos HH.

RNA. 2005 Oct;11(10):1494-504.PMID: 16199760 [PubMed - indexed for MEDLINE]Related articlesFree article

RNA pseudoknot prediction in energy-based models.

Lyngsø RB, Pedersen CN.

J Comput Biol. 2000;7(3-4):409-27.PMID: 11108471 [PubMed - indexed for MEDLINE]Related articles

KnotSeeker: heuristic pseudoknot detection in long RNA sequences.

Sperschneider J, Datta A.

RNA. 2008 Apr;14(4):630-40. Epub 2008 Feb 26.PMID: 18314500 [PubMed - indexed for MEDLINE]Related articlesFree article

Memory efficient alignment between RNA sequences and stochastic grammar models of pseudoknots.

Song Y, Liu C, Malmberg RL, He C, Cai L.

Int J Bioinform Res Appl. 2006;2(3):289-304.PMID: 18048167 [PubMed - indexed for MEDLINE]Related articles

Prediction of consensus RNA secondary structures including pseudoknots.

Witwer C, Hofacker IL, Stadler PF.

IEEE/ACM Trans Comput Biol Bioinform. 2004 Apr-Jun;1(2):66-77.PMID: 17048382 [PubMed - indexed for MEDLINE]Related articles

Predicting RNA secondary structures with arbitrary pseudoknots by maximizing the number of stacking pairs.

Ieong S, Kao MY, Lam TW, Sung WK, Yiu SM.

J Comput Biol. 2003;10(6):981-95.PMID: 14980021 [PubMed - indexed for MEDLINE]Related articles

An RNA folding algorithm including pseudoknots based on dynamic weighted matching.

Liu H, Xu D, Shao J, Wang Y.

Comput Biol Chem. 2006 Feb;30(1):72-6.PMID: 16321572 [PubMed - indexed for MEDLINE]Related articles

Rapid ab initio prediction of RNA pseudoknots via graph tree decomposition.

Zhao J, Malmberg RL, Cai L.

J Math Biol. 2008 Jan;56(1-2):145-59. Epub 2007 Sep 29.PMID: 17906862 [PubMed - indexed for MEDLINE]Related articles

[An iterative method for prediction of RNA secondary structures including pseudoknots based on minimum of free energy and covariance]

Wang ZX, Luo ZG, Guan NY, Yan FM, Jin X, Zhang W.

Yi Chuan. 2007 Jul;29(7):889-97. Chinese. PMID: 17646157 [PubMed - indexed for MEDLINE]Related articles

A partition function algorithm for nucleic acid secondary structure including pseudoknots.

Dirks RM, Pierce NA.

J Comput Chem. 2003 Oct;24(13):1664-77.PMID: 12926009 [PubMed - indexed for MEDLINE]Related articles

FlexStem: improving predictions of RNA secondary structures with pseudoknots by reducing the search space.

Chen X, He SM, Bu D, Zhang F, Wang Z, Chen R, Gao W.

Bioinformatics. 2008 Sep 15;24(18):1994-2001. Epub 2008 Jun 27.PMID: 18586700 [PubMed - indexed for MEDLINE]Related articlesFree article

Parsing nucleic acid pseudoknotted secondary structure: algorithm and applications.

Rastegari B, Condon A.

J Comput Biol. 2007 Jan-Feb;14(1):16-32.PMID: 17381343 [PubMed - indexed for MEDLINE]Related articles

Prediction of RNA secondary structure with pseudoknots using integer programming.

Poolsap U, Kato Y, Akutsu T.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S38.PMID: 19208139 [PubMed - indexed for MEDLINE]Related articlesFree article

An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots.

Ruan J, Stormo GD, Zhang W.

Bioinformatics. 2004 Jan 1;20(1):58-66.PMID: 14693809 [PubMed - indexed for MEDLINE]Related articlesFree article

An efficient method for the prediction of deleterious multiple-point mutations in the secondary structure of RNAs using suboptimal folding solutions.

Churkin A, Barash D.

BMC Bioinformatics. 2008 Apr 29;9:222.PMID: 18445289 [PubMed - indexed for MEDLINE]Related articlesFree article

Novel and efficient RNA secondary structure prediction using hierarchical folding.

Jabbari H, Condon A, Zhao S.

J Comput Biol. 2008 Mar;15(2):139-63.PMID: 18312147 [PubMed - indexed for MEDLINE]Related articles

Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures.

Matsui H, Sato K, Sakakibara Y.

Proc IEEE Comput Syst Bioinform Conf. 2004:290-9.PMID: 16448022 [PubMed - indexed for MEDLINE]Related articles

The computer simulation of RNA folding involving pseudoknot formation.

Gultyaev AP.

Nucleic Acids Res. 1991 May 11;19(9):2489-94.PMID: 1710358 [PubMed - indexed for MEDLINE]Related articlesFree article