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Results: 1 to 20 of 118

1.

The four ingredients of single-sequence RNA secondary structure prediction. A unifying perspective.

Rivas E.

RNA Biol. 2013 Jul;10(7):1185-96. doi: 10.4161/rna.24971. Epub 2013 May 10.

PMID:
23695796
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more.

Rivas E, Lang R, Eddy SR.

RNA. 2012 Feb;18(2):193-212. doi: 10.1261/rna.030049.111. Epub 2011 Dec 22.

PMID:
22194308
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

CONTRAfold: RNA secondary structure prediction without physics-based models.

Do CB, Woods DA, Batzoglou S.

Bioinformatics. 2006 Jul 15;22(14):e90-8.

PMID:
16873527
[PubMed - indexed for MEDLINE]
Free Article
4.

Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction.

Dowell RD, Eddy SR.

BMC Bioinformatics. 2004 Jun 4;5:71.

PMID:
15180907
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Evaluation of a sophisticated SCFG design for RNA secondary structure prediction.

Nebel ME, Scheid A.

Theory Biosci. 2011 Dec;130(4):313-36. doi: 10.1007/s12064-011-0139-7. Epub 2011 Dec 2.

PMID:
22135038
[PubMed - indexed for MEDLINE]
6.

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. doi: 10.1007/978-1-62703-709-9_8.

PMID:
24639159
[PubMed - indexed for MEDLINE]
7.

Accelerated probabilistic inference of RNA structure evolution.

Holmes I.

BMC Bioinformatics. 2005 Mar 24;6:73.

PMID:
15790387
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Evaluating the effect of disturbed ensemble distributions on SCFG based statistical sampling of RNA secondary structures.

Scheid A, Nebel ME.

BMC Bioinformatics. 2012 Jul 9;13:159. doi: 10.1186/1471-2105-13-159.

PMID:
22776037
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
21507242
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
19933322
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction.

Janssen S, Schudoma C, Steger G, Giegerich R.

BMC Bioinformatics. 2011 Nov 3;12:429. doi: 10.1186/1471-2105-12-429.

PMID:
22051375
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Simultaneous prediction of RNA secondary structure and helix coaxial stacking.

Shareghi P, Wang Y, Malmberg R, Cai L.

BMC Genomics. 2012 Jun 11;13 Suppl 3:S7. doi: 10.1186/1471-2164-13-S3-S7.

PMID:
22759616
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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:S22. doi: 10.1186/1471-2105-14-S2-S22. Epub 2013 Jan 21.

PMID:
23368905
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

SARNA-Predict: accuracy improvement of RNA secondary structure prediction using permutation-based simulated annealing.

Tsang HH, Wiese KC.

IEEE/ACM Trans Comput Biol Bioinform. 2010 Oct-Dec;7(4):727-40. doi: 10.1109/TCBB.2008.97.

PMID:
21030739
[PubMed - indexed for MEDLINE]
15.

Frnakenstein: multiple target inverse RNA folding.

Lyngsø RB, Anderson JW, Sizikova E, Badugu A, Hyland T, Hein J.

BMC Bioinformatics. 2012 Oct 9;13:260. doi: 10.1186/1471-2105-13-260.

PMID:
23043260
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Enhancement of accuracy and efficiency for RNA secondary structure prediction by sequence segmentation and MapReduce.

Zhang B, Yehdego DT, Johnson KL, Leung MY, Taufer M.

BMC Struct Biol. 2013;13 Suppl 1:S3. doi: 10.1186/1472-6807-13-S1-S3. Epub 2013 Nov 8.

PMID:
24564983
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments.

Seemann SE, Gorodkin J, Backofen R.

Nucleic Acids Res. 2008 Nov;36(20):6355-62. doi: 10.1093/nar/gkn544. Epub 2008 Oct 4.

PMID:
18836192
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

GTfold: enabling parallel RNA secondary structure prediction on multi-core desktops.

Swenson MS, Anderson J, Ash A, Gaurav P, Sükösd Z, Bader DA, Harvey SC, Heitsch CE.

BMC Res Notes. 2012 Jul 2;5:341. doi: 10.1186/1756-0500-5-341.

PMID:
22747589
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Consensus folding of unaligned RNA sequences revisited.

Bafna V, Tang H, Zhang S.

J Comput Biol. 2006 Mar;13(2):283-95.

PMID:
16597240
[PubMed - indexed for MEDLINE]
20.

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
[PubMed - indexed for MEDLINE]
Free Article

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