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Created on: 06-Aug-2012   Last updated on: 10-Nov-2012 |  How to cite this?
Total resources - 20
A compilation of RNA structure prediction resources
Ramya G (Correspondence: Acharya KK, kshitish@ibab.ac.in)

Resources

Important features / utilities*CitationsYear of publicationRank by usage frequency Add comments
Mfold
http://mfold.rna.albany.edu/?q=mfold
Mfold is a pioneer tool for RNA structure predictions. It uses minimum free energy (MFE) dynamic programming algorithm to calculate secondary structures of RNA.
Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003 Jul 1;31(13):3406-15. PubMed PMID: 12824337; PubMed Central PMCID: PMC169194 Waugh A, Gendron P, Altman R, Brown JW, Case D, Gautheret D, Harvey SC,Leontis N, Westbrook J, Westhof E, Zuker M, Major F. RNAML: a standard syntax for exchanging RNA information. RNA. 2002 Jun;8(6):707-17. PubMed PMID: 12088144; PubMed Central PMCID: PMC1370290. Zuker M, Jacobson AB. Using reliability information to annotate RNA secondary structures. RNA. 1998 Jun;4(6):669-79. PubMed PMID: 9622126; PubMed Central PMCID: PMC1369649.
2003
18
Vienna RNA Package
http://rna.tbi.univie.ac.at/
Apart from free energy minimization, this package uses partition function calculations, stochastic sampling and maximum expected accuracy structure prediction.
Hofacker IL, Fontana W, Stadler PF, Bonhoeffer LS, Tacker M, Schuste P. Fast folding and comparison of RNA secondary structures. Monatshefte für Chemie. 1994;125:167-188. Hofacker IL. Vienna RNA secondary structure server. Nucleic Acids Res. 2003 Jul 1;31(13):3429-31. PubMed PMID: 12824340; PubMed Central PMCID: PMC169005. Lorenz R, Bernhart SH, Höner Zu Siederdissen C, Tafer H, Flamm C, Stadler PF, Hofacker IL. ViennaRNA Package 2.0. Algorithms Mol Biol. 2011 Nov 24;6:26. PubMed PMID: 22115189; PubMed Central PMCID: PMC3319429.
2003
50
UNAFold
http://mfold.rit.albany.edu/?q=DINAMelt/software
UNAFold/Unified Nucleic Acid Folding and hybridization package combines free energy minimization, partition function calculations and stochastic sampling to derive stable RNA structures.
Markham NR, Zuker M. UNAFold: software for nucleic acid folding and hybridization. Methods Mol Biol. 2008;453:3-31. PubMed PMID: 18712296. Zuker M, Mathews DH & Turner DH. Algorithms and thermodynamics for RNA secondary structure prediction: A practical guide in RNA biochemistry and biotechnology. NATO ASI Series. 1999; 11-43. Zuker M. Prediction of RNA secondary structure by energy minimization. Methods Mol Biol. 1994;25:267-94. PubMed PMID: 7516239. Jaeger JA, Turner DH, Zuker M. Predicting optimal and suboptimal secondary structure for RNA. Methods Enzymol. 1990;183:281-306. PubMed PMID: 1690335. Zuker M. On finding all suboptimal foldings of an RNA molecule. Science. 1989 Apr 7;244(4900):48-52. Review. PubMed PMID: 2468181.
2008
63
RNAstructure
http://rna.urmc.rochester.edu/rnastructure.html
RNAStructure uses a wide range of algorithms including free energy minimization, partition function calculations, stochastic sampling, maximum expected accuracy structure prediction and others.
Reuter JS, Mathews DH. RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinformatics. 2010 Mar 15;11:129. PubMed PMID: 20230624; PubMed Central PMCID: PMC2984261. Mathews DH. RNA secondary structure analysis using RNAstructure. Curr Protoc Bioinformatics. 2006 Mar;Chapter 12:Unit 12.6. PubMed PMID: 18428759.
2006
91
MC-Fold/MC-Cons
http://www.major.iric.ca/MC-Pipeline/
It is based on nucleotide cyclic motifs' algorithms that considers all base-pairing interactions apart from A.U, G.C & G.U.
Parisien M, Major F. The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature. 2008 Mar 6;452(7183):51-5. PubMed PMID: 18322526.
2007
95
Pknots
http://selab.janelia.org/software.html
It uses a dynamic programming algorithm for predicting optimal RNA secondary structure, including pseudoknots.
Rivas E, Eddy SR. A dynamic programming algorithm for RNA structure prediction including pseudoknots. J Mol Biol. 1999 Feb 5;285(5):2053-68. PubMed PMID: 9925784.
1999
95
Sfold
http://sfold.wadsworth.org/cgi-bin/index.pl
It is based on statistical sampling paradigm.
Ding Y, Chan CY, Lawrence CE. Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W135-41. PubMed PMID: 15215366; PubMed Central PMCID: PMC441587.
2004
96
Pfold
http://daimi.au.dk/~compbio/pfold/
Pfold uses stochastic context free grammars and evolutionary models.
Knudsen B, Hein JJ. Using stochastic context free grammars and molecular evolution to predict RNA secondary structure. Bioinformatics. 1999; 15 (6), 446-454. Knudsen B, Hein J. Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res. 2003 Jul 1;31(13):3423-8. PubMed PMID: 12824339; PubMed Central PMCID: PMC169020.
1999
96
CONTRAfold
http://contra.stanford.edu/contrafold/
It is based on probabilistic models built upon stochastic context-free grammars called conditional log-linear models (CLLMs).
Do CB, Foo CS, Batzoglou S. A max-margin model for efficient simultaneous alignment and folding of RNA sequences. Bioinformatics. 2008 Jul 1;24(13):i68-76. PubMed PMID: 18586747; PubMed Central PMCID: PMC2718655. Do CB, Woods DA, Batzoglou S. CONTRAfold: RNA secondary structure prediction without physics-based models. Bioinformatics. 2006 Jul 15;22(14):e90-8. PubMed PMID: 16873527.
2006
96
EvoFold
www.cbse.ucsc.edu/jsp/EvoFold
EvoFold uses comparative genomics based on phylogenetic stochastic context-free grammars for identifying conserved functional RNAs.
Pedersen JS, Bejerano G, Siepel A, Rosenbloom K, Lindblad-Toh K, Lander ES, Kent J, Miller W, Haussler D. Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol. 2006 Apr;2(4):e33. Epub 2006 Apr 21. PubMed PMID: 16628248; PubMed Central PMCID: PMC1440920.
2006
97
CentroidFold
http://www.ncrna.org/centroidfold/
It uses averaged gamma-centroid estimator, which is a combination of sFold (centroid) and CONTRAfold (MEA).
Hamada M, Kiryu H, Sato K, Mituyama T, Asai K. Prediction of RNA secondary structure using generalized centroid estimators. Bioinformatics. 2009 Feb 15;25(4):465-73. Epub 2008 Dec 18. PubMed PMID: 19095700. Sato K, Hamada M, Asai K, Mituyama T. CENTROIDFOLD: a web server for RNA secondary structure prediction. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W277-80. Epub 2009 May 12. PubMed PMID: 19435882; PubMed Central PMCID: PMC2703931.
2009
97
RNAshapes
http://bibiserv.techfak.uni-bielefeld.de/rnashapes/
RNAshapes integrates shape abstraction with MFE dynamic programming algorithms.
Steffen P, Voss B, Rehmsmeier M, Reeder J, Giegerich R. RNAshapes: an integrated RNA analysis package based on abstract shapes. Bioinformatics. 2006 Feb 15;22(4):500-3. Epub 2005 Dec 15. PubMed PMID: 16357029.
2006
98
Foldalign
http://foldalign.ku.dk/
It is based on a lightweight energy model and sequence similarity. It implements the Sankoff algorithm for simultaneous structural alignment of multiple sequences.
Havgaard JH, Torarinsson E, Gorodkin J. Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix. PLoS Comput Biol. 2007 Oct;3(10):1896-908. Epub 2007 Aug 20. PubMed PMID: 17937495; PubMed Central PMCID: PMC2014794. Torarinsson E, Havgaard JH, Gorodkin J. Multiple structural alignment and clustering of RNA sequences. Bioinformatics. 2007 Apr 15;23(8):926-32. Epub 2007 Feb 25. PubMed PMID: 17324941. Havgaard JH, Lyngsø RB, Gorodkin J. The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W650-3. PubMed PMID: 15980555; PubMed Central PMCID: PMC1160234.
2005
98
Kinefold
http://kinefold.curie.fr/
Its results are based on stochastic folding simulations.
Xayaphoummine A, Bucher T, Isambert H. Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W605-10. PubMed PMID: 15980546; PubMed Central PMCID: PMC1160208.
2005
98
Ppfold
http://daimi.au.dk/~compbio/pfold/downloads.html
Ppfold uses stochastic context free grammars and evolutionary models.
Sükösd Z, Knudsen B, Kjems J, Pedersen CN. PPfold 3.0: fast RNA secondary structure prediction using phylogeny and auxiliary data. Bioinformatics. 2012 Oct 15;28(20):2691-2. doi: 10.1093/bioinformatics/bts488. Epub 2012 Aug 9. PubMed PMID: 22877864. Sükösd Z, Knudsen B, Vaerum M, Kjems J, Andersen ES. Multithreaded comparative RNA secondary structure prediction using stochastic context-free grammars. BMC Bioinformatics. 2011 Apr 18;12:103. PubMed PMID: 21501497; PubMed Central PMCID: PMC3102635.
2012
100
CentroidHomfold
http://www.ncrna.org/centroidhomfold
It is based on posterior decoding techniques, which consider all the suboptimal secondary structures of the target and homologous sequences and all the suboptimal alignments between the target sequence and each of the homologous sequences.
Hamada M, Sato K, Kiryu H, Mituyama T, Asai K. Predictions of RNA secondary structure by combining homologous sequence information. Bioinformatics. 2009 Jun 15;25(12):i330-8. PubMed PMID: 19478007; PubMed Central PMCID: PMC2687982. Frith MC, Hamada M, Horton P. Parameters for accurate genome alignment. BMC Bioinformatics. 2010 Feb 9;11:80. PubMed PMID: 20144198; PubMed Central PMCID: PMC2829014. Hamada M, Yamada K, Sato K, Frith MC, Asai K. CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W100-6. Epub 2011 May 11. PubMed PMID: 21565800; PubMed Central PMCID: PMC3125741.
2009
100
RSmatch
http://exon.umdnj.edu/RSmatch/
It aligns RNA secondary structures and finds RNA motifs using position dependent and position independent scoring matrices.
Liu J, Wang JT, Hu J, Tian B. A method for aligning RNA secondary structures and its application to RNA motif detection. BMC Bioinformatics. 2005 Apr 7;6:89. PubMed PMID: 15817128; PubMed Central PMCID: PMC1090556.
2005
100
CyloFold
http://cylofold.abcc.ncifcrf.gov/
It is based on placement of helices allowing complex pseudoknots.
Bindewald E, Kluth T, Shapiro BA. CyloFold: secondary structure prediction including pseudoknots. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W368-72. Epub 2010 May 25. PubMed PMID: 20501603; PubMed Central PMCID: PMC2896150.
2010
100
Crumple
http://adenosine.chem.ou.edu/software.html
It is built to generate secondary structures for satellite tobacco mosaic virus (STV) particle, in consistent with the available crystallographic structure.
Schroeder SJ, Stone JW, Bleckley S, Gibbons T, Mathews DM. Ensemble of secondary structures for encapsidated satellite tobacco mosaic virus RNA consistent with chemical probing and crystallography constraints. Biophys J. 2011 Jul 6;101(1):167-75. PubMed PMID: 21723827; PubMed Central PMCID: PMC3127170.
2011
100
RNA123
http://www.rna123.com/
It is based on homology modelling.
Not available
Not available
100
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