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Items: 1 to 20 of 285

1.

Predicting pseudoknotted structures across two RNA sequences.

Sperschneider J, Datta A, Wise MJ.

Bioinformatics. 2012 Dec 1;28(23):3058-65. doi: 10.1093/bioinformatics/bts575. Epub 2012 Oct 8.

2.

DotKnot: pseudoknot prediction using the probability dot plot under a refined energy model.

Sperschneider J, Datta A.

Nucleic Acids Res. 2010 Apr;38(7):e103. doi: 10.1093/nar/gkq021. Epub 2010 Jan 31.

3.

Heuristic RNA pseudoknot prediction including intramolecular kissing hairpins.

Sperschneider J, Datta A, Wise MJ.

RNA. 2011 Jan;17(1):27-38. doi: 10.1261/rna.2394511. Epub 2010 Nov 22.

4.

A fast and robust iterative algorithm for prediction of RNA pseudoknotted secondary structures.

Jabbari H, Condon A.

BMC Bioinformatics. 2014 May 18;15:147. doi: 10.1186/1471-2105-15-147.

5.

A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences.

Ji Y, Xu X, Stormo GD.

Bioinformatics. 2004 Jul 10;20(10):1591-602. Epub 2004 Feb 12.

PMID:
14962926
6.

Improved free energy parameters for RNA pseudoknotted secondary structure prediction.

Andronescu MS, Pop C, Condon AE.

RNA. 2010 Jan;16(1):26-42. doi: 10.1261/rna.1689910. Epub 2009 Nov 20.

7.

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
8.

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. doi: 10.1186/1471-2105-10-S1-S38.

9.

Thermodynamic heuristics with case-based reasoning: combined insights for RNA pseudoknot secondary structure.

Al-Khatib RM, Rashid NA, Abdullah R.

J Biomol Struct Dyn. 2011 Aug;29(1):1-26.

PMID:
21696223
10.

Predictions of RNA secondary structure by combining homologous sequence information.

Hamada M, Sato K, Kiryu H, Mituyama T, Asai K.

Bioinformatics. 2009 Jun 15;25(12):i330-8. doi: 10.1093/bioinformatics/btp228.

11.

IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming.

Sato K, Kato Y, Hamada M, Akutsu T, Asai K.

Bioinformatics. 2011 Jul 1;27(13):i85-93. doi: 10.1093/bioinformatics/btr215.

12.

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. doi: 10.1093/bioinformatics/btn327. Epub 2008 Jun 27.

PMID:
18586700
13.

DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition.

Sato K, Kato Y, Akutsu T, Asai K, Sakakibara Y.

Bioinformatics. 2012 Dec 15;28(24):3218-24. doi: 10.1093/bioinformatics/bts612. Epub 2012 Oct 11.

PMID:
23060618
14.

Bayesian sampling of evolutionarily conserved RNA secondary structures with pseudoknots.

Doose G, Metzler D.

Bioinformatics. 2012 Sep 1;28(17):2242-8. doi: 10.1093/bioinformatics/bts369. Epub 2012 Jul 13.

PMID:
22796961
15.

TurboFold: iterative probabilistic estimation of secondary structures for multiple RNA sequences.

Harmanci AO, Sharma G, Mathews DH.

BMC Bioinformatics. 2011 Apr 20;12:108. doi: 10.1186/1471-2105-12-108.

16.

KnotSeeker: heuristic pseudoknot detection in long RNA sequences.

Sperschneider J, Datta A.

RNA. 2008 Apr;14(4):630-40. doi: 10.1261/rna.968808. Epub 2008 Feb 26.

17.

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. doi: 10.1089/cmb.2007.0198.

PMID:
18312147
18.

RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment.

Xu X, Ji Y, Stormo GD.

Bioinformatics. 2007 Aug 1;23(15):1883-91. Epub 2007 May 30.

PMID:
17537756
19.

Energy-based RNA consensus secondary structure prediction in multiple sequence alignments.

Washietl S, Bernhart SH, Kellis M.

Methods Mol Biol. 2014;1097:125-41. doi: 10.1007/978-1-62703-709-9_7. Review.

PMID:
24639158
20.

HotKnots: heuristic prediction of RNA secondary structures including pseudoknots.

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

RNA. 2005 Oct;11(10):1494-504.

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