116 related articles for article (PubMed ID: 22877864)
1. PPfold 3.0: fast RNA secondary structure prediction using phylogeny and auxiliary data.
Sükösd Z; Knudsen B; Kjems J; Pedersen CN
Bioinformatics; 2012 Oct; 28(20):2691-2. PubMed ID: 22877864
[TBL] [Abstract][Full Text] [Related]
2. Multithreaded comparative RNA secondary structure prediction using stochastic context-free grammars.
Sükösd Z; Knudsen B; Vaerum M; Kjems J; Andersen ES
BMC Bioinformatics; 2011 Apr; 12():103. PubMed ID: 21501497
[TBL] [Abstract][Full Text] [Related]
3. Characterising RNA secondary structure space using information entropy.
Sükösd Z; Knudsen B; Anderson JW; Novák A; Kjems J; Pedersen CN
BMC Bioinformatics; 2013; 14 Suppl 2(Suppl 2):S22. PubMed ID: 23368905
[TBL] [Abstract][Full Text] [Related]
4. Pfold: RNA secondary structure prediction using stochastic context-free grammars.
Knudsen B; Hein J
Nucleic Acids Res; 2003 Jul; 31(13):3423-8. PubMed ID: 12824339
[TBL] [Abstract][Full Text] [Related]
5. StatAlign 2.0: combining statistical alignment with RNA secondary structure prediction.
Arunapuram P; Edvardsson I; Golden M; Anderson JW; Novák A; Sükösd Z; Hein J
Bioinformatics; 2013 Mar; 29(5):654-5. PubMed ID: 23335014
[TBL] [Abstract][Full Text] [Related]
6. Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data.
Wu Y; Shi B; Ding X; Liu T; Hu X; Yip KY; Yang ZR; Mathews DH; Lu ZJ
Nucleic Acids Res; 2015 Sep; 43(15):7247-59. PubMed ID: 26170232
[TBL] [Abstract][Full Text] [Related]
7. CONTRAfold: RNA secondary structure prediction without physics-based models.
Do CB; Woods DA; Batzoglou S
Bioinformatics; 2006 Jul; 22(14):e90-8. PubMed ID: 16873527
[TBL] [Abstract][Full Text] [Related]
8. RNAstructure: software for RNA secondary structure prediction and analysis.
Reuter JS; Mathews DH
BMC Bioinformatics; 2010 Mar; 11():129. PubMed ID: 20230624
[TBL] [Abstract][Full Text] [Related]
9. RNA-TVcurve: a Web server for RNA secondary structure comparison based on a multi-scale similarity of its triple vector curve representation.
Li Y; Shi X; Liang Y; Xie J; Zhang Y; Ma Q
BMC Bioinformatics; 2017 Jan; 18(1):51. PubMed ID: 28109252
[TBL] [Abstract][Full Text] [Related]
10. SCFGs in RNA secondary structure prediction RNA secondary structure prediction: a hands-on approach.
Sükösd Z; Andersen ES; Lyngsø R
Methods Mol Biol; 2014; 1097():143-62. PubMed ID: 24639159
[TBL] [Abstract][Full Text] [Related]
11. Experiment-Assisted Secondary Structure Prediction with RNAstructure.
Xu ZZ; Mathews DH
Methods Mol Biol; 2016; 1490():163-76. PubMed ID: 27665598
[TBL] [Abstract][Full Text] [Related]
12. Quantifying variances in comparative RNA secondary structure prediction.
Anderson JW; Novák Á; Sükösd Z; Golden M; Arunapuram P; Edvardsson I; Hein J
BMC Bioinformatics; 2013 May; 14():149. PubMed ID: 23634662
[TBL] [Abstract][Full Text] [Related]
13. ProbFold: a probabilistic method for integration of probing data in RNA secondary structure prediction.
Sahoo S; Świtnicki MP; Pedersen JS
Bioinformatics; 2016 Sep; 32(17):2626-35. PubMed ID: 27153612
[TBL] [Abstract][Full Text] [Related]
14. Modeling RNA Secondary Structure with Sequence Comparison and Experimental Mapping Data.
Tan Z; Sharma G; Mathews DH
Biophys J; 2017 Jul; 113(2):330-338. PubMed ID: 28735622
[TBL] [Abstract][Full Text] [Related]
15. Secondary Structure Prediction of Single Sequences Using RNAstructure.
Xu ZZ; Mathews DH
Methods Mol Biol; 2016; 1490():15-34. PubMed ID: 27665590
[TBL] [Abstract][Full Text] [Related]
16. 4SALE--a tool for synchronous RNA sequence and secondary structure alignment and editing.
Seibel PN; Müller T; Dandekar T; Schultz J; Wolf M
BMC Bioinformatics; 2006 Nov; 7():498. PubMed ID: 17101042
[TBL] [Abstract][Full Text] [Related]
17. Dynalign II: common secondary structure prediction for RNA homologs with domain insertions.
Fu Y; Sharma G; Mathews DH
Nucleic Acids Res; 2014 Dec; 42(22):13939-48. PubMed ID: 25416799
[TBL] [Abstract][Full Text] [Related]
18. Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction.
Dowell RD; Eddy SR
BMC Bioinformatics; 2004 Jun; 5():71. PubMed ID: 15180907
[TBL] [Abstract][Full Text] [Related]
19. iFoldRNA v2: folding RNA with constraints.
Krokhotin A; Houlihan K; Dokholyan NV
Bioinformatics; 2015 Sep; 31(17):2891-3. PubMed ID: 25910700
[TBL] [Abstract][Full Text] [Related]
20. Predicting the secondary structure common to two RNA sequences with Dynalign.
Mathews D
Curr Protoc Bioinformatics; 2004 Dec; Chapter 12():Unit 12.4. PubMed ID: 18428718
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
