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A simple, practical and complete O(n3/log n)-time algorithm for RNA folding using the Four-Russians speedup.

Frid Y, Gusfield D.

Algorithms Mol Biol. 2010 Jan 4;5:13.PMID: 20047670 [PubMed]Free PMC ArticleFree textRelated citations

A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure.

Eddy SR.

BMC Bioinformatics. 2002 Jul 2;3:18.PMID: 12095421 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Speeding up the dynamic algorithm for planar RNA folding.

Nussinov R, Shapiro B, Le SY, Maizel JV Jr.

Math Biosci. 1990 Jun;100(1):33-47.PMID: 1724937 [PubMed - indexed for MEDLINE]Related citations

RNAslider: a faster engine for consecutive windows folding and its application to the analysis of genomic folding asymmetry.

Horesh Y, Wexler Y, Lebenthal I, Ziv-Ukelson M, Unger R.

BMC Bioinformatics. 2009 Mar 4;10:76.PMID: 19257906 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

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]Free PMC ArticleFree textRelated citations

Prediction of common folding structures of homologous RNAs.

Han K, Kim HJ.

Nucleic Acids Res. 1993 Mar 11;21(5):1251-7.PMID: 7681944 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

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 citations

Fast index based algorithms and software for matching position specific scoring matrices.

Beckstette M, Homann R, Giegerich R, Kurtz S.

BMC Bioinformatics. 2006 Aug 24;7:389.PMID: 16930469 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

A Faster Algorithm for Simultaneous Alignment and Folding of RNA.

Ziv-Ukelson M, Gat-Viks I, Wexler Y, Shamir R.

J Comput Biol. 2010 Jul 22. [Epub ahead of print]PMID: 20649420 [PubMed - as supplied by publisher]Related citations

An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem.

Shmygelska A, Hoos HH.

BMC Bioinformatics. 2005 Feb 14;6:30.PMID: 15710037 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

A linear-time algorithm for the perfect phylogeny haplotyping (PPH) problem.

Ding Z, Filkov V, Gusfield D.

J Comput Biol. 2006 Mar;13(2):522-53.PMID: 16597255 [PubMed - indexed for MEDLINE]Related citations

Rnall: an efficient algorithm for predicting RNA local secondary structural landscape in genomes.

Wan XF, Lin G, Xu D.

J Bioinform Comput Biol. 2006 Oct;4(5):1015-31.PMID: 17099939 [PubMed - indexed for MEDLINE]Related citations

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]Free PMC ArticleFree textRelated citations

Graphical exploratory data analysis of RNA secondary structure dynamics predicted by the massively parallel genetic algorithm.

Shapiro BA, Kasprzak W, Grunewald C, Aman J.

J Mol Graph Model. 2006 Dec;25(4):514-31. Epub 2006 Apr 28.PMID: 16725358 [PubMed - indexed for MEDLINE]Related citations

Versatile and declarative dynamic programming using pair algebras.

Steffen P, Giegerich R.

BMC Bioinformatics. 2005 Sep 12;6:224. Erratum in: BMC Bioinformatics. 2006;7:214. PMID: 16156887 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

A study of accessible motifs and RNA folding complexity.

Wexler Y, Zilberstein C, Ziv-Ukelson M.

J Comput Biol. 2007 Jul-Aug;14(6):856-72.PMID: 17691898 [PubMed - indexed for MEDLINE]Related citations

Fast and memory efficient implementation of the exact PNN.

Fränti P, Kaukoranta T, Shen DF, Chang KS.

IEEE Trans Image Process. 2000;9(5):773-7.PMID: 18255449 [PubMed]Related citations

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]Free PMC ArticleFree textRelated citations

Improving the practical space and time efficiency of the shortest-paths approach to sum-of-pairs multiple sequence alignment.

Gupta SK, Kececioglu JD, Schäffer AA.

J Comput Biol. 1995 Fall;2(3):459-72.PMID: 8521275 [PubMed - indexed for MEDLINE]Related citations

Transforming rooted agreement into unrooted agreement.

Przytycka TM.

J Comput Biol. 1998 Summer;5(2):335-49.PMID: 9672836 [PubMed - indexed for MEDLINE]Related citations