RNA folding with hard and soft constraints

Algorithms for Molecular Biology

Volumn 11, Issue 1, 2016, Pages

  Lorenz, Ronny ^a   Hofacker, Ivo L ^a,b   Stadler, Peter F ^a,b,c,d,e,f  

^a UNIVERSITY OF VIENNA   (Austria)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

^c UNIVERSITY OF LEIPZIG   (Germany)

^d MAX PLANCK INSTITUTE FOR MATHEMATICS IN THE SCIENCES   (Germany)

^e FRAUNHOFER INSTITUTE FOR CELL THERAPY AND IMMUNOLOGY   (Germany)

^f SANTA FE INSTITUTE   (United States)

Author keywords

Constraints; Dynamic programming; RNA folding

Indexed keywords

EID: 85007493448     PISSN: None     EISSN: 17487188     Source Type: Journal    
DOI: 10.1186/S13015-016-0070-Z     Document Type: Article

References (58)

1. Doshi K, Cannone J, Cobaugh C, Gutell R. Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction. BMC Bioinform. 2004;5:105.
2. Hajiaghayi M, Condon A, Hoos HH. Analysis of energy-based algorithms for RNA secondary structure prediction. BMC Bioinform. 2012;13:22.
3. Dowell RD, Eddy SR. Evaluation of several lightweight stochastic contextfree grammars for RNA secondary structure prediction. BMC Bioinform. 2004;5:7.
4. Nebel ME, Scheid A. Evaluation of a sophisticated SCFG design for RNA secondary structure prediction. Theory Biosci. 2011;130:313-36.
5. Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci USA. 2004;101:7287-92.
6. Gaspin C, Westhof E. An interactive framework for RNA secondary structure prediction with a dynamical treatment of constraints. J Mol Biol. 1995;254:163-74.
7. Zuker M, Stiegler P. Optimal computer folding of large rna sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 1981;9:133-48.
8. Hofacker IL, Fontana W, Stadler PF, Bonhoeffer LS, Tacker M, Schuster P. Fast folding and comparison of RNA secondary structures. Mon Chem. 1994;125:167-88.
9. Zuker M. On finding all suboptimal foldings of an RNA molecule. Science. 1989;244:48-52.
10. Reeder J, Giegerich R. Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. BMC Bioinform. 2004;5:104.
11. Reeder J, Reeder J, Giegerich R. Locomotif: from graphical motif description to RNA motif search. Bioinformatics. 2007;23:392-400.
12. Giegerich R, Meyer C, Steffen P. A discipline of dynamic programming over sequence data. Sci Comput Program. 2004;51:215-63.
13. Giegerich R, Voß B, Rehmsmeier M. Abstract shapes of RNA. Nucleic Acids Res. 2004;32:4843-51.
14. Mückstein U, Tafer H, Hackermüller J, Bernhard SB, Stadler PF, Hofacker IL. Thermodynamics of RNA-RNA binding. Bioinformatics. 2006;22:1177-82.
15. Busch A, Richter AS, Backofen R. IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinformatics. 2008;24:2849-56.
16. Chitsaz H, Backofen R, Sahinalp SC. biRNA: Fast RNA-RNA binding sites prediction. In Proc of the 9th Workshop on Algorithms in Bioinformatics (WABI). Berlin: Springer; 2009. p. 25-36.
17. Forties RA, Bundschuh R. Modeling the interplay of single stranded binding proteins and nucleic acid secondary structure. Bioinformatics. 2010;26(1):61-7.
18. Wachsmuth M, Findeiß S, Weissheimer N, Stadler PF, Mörl M. De novo design of a synthetic riboswitch that regulates transcription termination. Nucleic Acids Res. 2013;41:2541-51.
19. Hofacker IL, Fekete M, Stadler PF. Secondary structure prediction for aligned RNA sequences. J Mol Biol. 2002;319:1059-66.
20. Bernhart SH, Hofacker IL, Will S, Gruber AR, Stadler PF. RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinforma. 2008;9:474.
21. Harmanci AO, Sharma G, Mathews DH. TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences. BMC Bioinform. 2011;12:108.
22. Deigan KE, Li TW, Mathews DH, Weeks KM. Accurate SHAPE-directed RNA structure determination. Proc Natl Acad Sci USA. 2009;106:97-102.
23. Zarringhalam K, Meyer MM, Dotu I, Chuang JH, Clote P. Integrating chemical footprinting data into RNA secondary structure prediction. PLoS ONE. 2012;7:45160.
24. Hajdin CE, Bellaousov S, Huggins W, Leonard CW, Mathews DH, Weeks KM. Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots. Proc Natl Acad Sci USA. 2013;110:5498-503.
25. Sükösd Z, Swenson MS, Kjems J, Heitsch CE. Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions. Nucleic Acids Res. 2013;41:2807-16.
26. Cordero P, Kladwang W, VanLang CC, Das R. Quantitative dimethyl sulfate mapping for automated RNA secondary structure inference. Biochemistry. 2012;51:7037-9.
27. Kertesz M, Wan Y, Mazor E, Rinn JL, Nutter RC, Chang HY, Segal E. Genome-wide measurement of RNA secondary structure in yeast. Nature. 2010;467:103-7.
28. Wan Y, Qu K, Zhang QC, Flynn RA, Manor O, Ouyang Z, Zhang J, Spitale RC, Snyder MP, Segal E, Chang HY. Landscape and variation of RNA secondary structure across the human transcriptome. Nature. 2014;505:706-9.
29. Washietl S, Hofacker IL, Stadler PF, Kellis M. RNA folding with soft constraints: Reconciliation of probing data and thermodynamic secondary structure prediction. Nucleic Acids Res. 2012;40:4261-72.
30. Helm M. Post-transcriptional nucleotide modification and alternative folding of RNA. Nucleic Acids Res. 2006;34:721-33.
31. Lorenz R, Bernhart SH, Höner zu Siederdissen C, Tafer H, Flamm C, Stadler PF, Hofacker IL. ViennaRNA Package 2.0. Alg Mol Biol. 2011;6:26.
32. Nussinov R, Piecznik G, Griggs JR, Kleitman DJ. Algorithms for loop matching. SIAM J Appl Math. 1978;35:68-82.
33. Rivas E, Eddy S. The language of RNA: a formal grammar that includes pseudoknots. Bioinformatics. 2000;16:334-40.
34. Reeder J, Giegerich R. Rna secondary structure analysis using the rnashapes package. Curr Protoc Bioinform. 2009;12:12-8. doi:10.1002/0471250953.bi1208s26.
35. Lange SJ, Maticzka D, Möhl M, Gagnon JN, Brown CM, Backofen R. Global or local? predicting secondary structure and accessibility in mRNAs. Nucleic Acids Res. 2012;40:5215-26.
36. Bernhart S, Hofacker IL, Stadler PF. Local RNA base pairing probabilities in large sequences. Bioinformatics. 2006;22:614-5.
37. Hofacker IL, Priwitzer B, Stadler PF. Prediction of locally stable RNA secondary structures for genome-wide surveys. Bioinformatics. 2004;20:191-8.
38. Proctor JR, Meyer IM. CoFold: an RNA secondary structure prediction method that takes co-transcriptional folding into account. Nucleic Acids Res. 2013;41:102.
39. Amman F, Bernhart SH, Doose G, Hofacker IL, Qin J, Stadler PF. The trouble with long-range base pairs in RNA folding. In: Setubal JC, Almeida NF, editors. Advances in bioinformatics and computational biology, 8th BSB. Lect. Notes Comp. Sci. vol. 8213. Berlin: Springer; 2013. p. 1-11.
40. Lorenz R, Bernhart SH, Qin J, Höner zu Siederdissen C, Tanzer A, Amman F, Hofacker IL, Stadler PF. 2D meets 4G: G-quadruplexes in RNA secondary structure prediction. IEEE Trans Comput Biol Bioinform. 2013;10:832-44. doi:10.1109/TCBB.2013.7.
41. Zuker M, Jaeger JA, Turner DH. A comparison of optimal and suboptimal RNA secondary structures predicted by free energy minimization with structures determined by phylogenetic comparison. Nucleic Acids Res. 1991;19:2707-14.
42. Lorenz R, Luntzer D, Hofacker IL, Stadler PF, Wolfinger MT. SHAPE directed RNA folding. Bioinformatics. 2015;145-147:32. doi:10.1093/bioinformatics/btv523.
43. Tacker M, Stadler PF, Bornberg-Bauer EG, Hofacker IL, Schuster P. Algorithm independent properties of RNA structure prediction. Eur Biophys J. 1996;25:115-30.
44. Ding Y, Lawrence CE. A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Res. 2003;31:7280-301.
45. Ponty Y. Efficient sampling of RNA secondary structures from the Boltzmann ensemble of low-energy: the boustrophedon method. J Math Biol. 2008;56:107-27.
46. Machnicka MA, Milanowska K, Osman Oglou O, Purta E, Kurkowska M, Olchowik A, Januszewski W, Kalinowski S, Dunin-Horkawicz S, Rother KM, Helm M, Bujnicki JM, Grosjean H. MODOMICS: a database of RNA modification pathways-2013 update. Nucleic Acids Res. 2013;41:262-7.
47. Motorin Y, Muller S, Behm-Ansmant I, Branlant C. Identification of modified residues in RNAs by reverse transcription-based methods. Methods Enzymol. 2007;425:21-53.
48. Voigts-Hoffmann F, Hengesbach M, Kobitski AY, Van Aerschot A, Herdewijn P, Nienhaus GU, Helm M. A methyl group controls conformational equilibrium in human mitochondrial tRNALys. J Am Chem Soc. 2007;129:13382-3.
49. Motorin Y, Helm M. tRNA stabilization by modified nucleotides. Biochemistry. 2010;49:4934-44.
50. Jühling F, Mörl M, Hartmann RK, Sprinzl M, Stadler PF, Pütz J. tRNAdb 2009: compilation of tRNA sequences and tRNA genes. Nucleic Acids Res. 2009;37:159-62.
51. Mortimer SA, Kidwell MA, Doudna JA. Insights into RNA structure and function from genome-wide studies. Nature Rev Genet. 2014;15:469-79.
52. Eddy SR. Computational analysis of conserved RNA secondary structure in transcriptomes and genomes. Annu Rev Biophys. 2014;43:433-56.
53. Breaker RR. Prospects for riboswitch discovery and analysis. Mol Cell. 2011;43:867-79.
54. Clingman CC, Ryder SP. Metabolite sensing in eukaryotic mRNA biology. Wiley Interdiscip Rev RNA. 2013;4:387-96.
55. Jenison RD, Gill SC, Pardi A, Polisky B. High-resolution molecular discrimination by RNA. Science. 1994;263:1425-9.
56. Wachsmuth M, Domin GD, Lorenz R, Serfling R, Findeiß S, Stadler PF, Mörl M. Design criteria for synthetic riboswitches acting on transcription. RNA Biol. 2015;12:221-31. doi:10.1080/15476286.2015.1017235.
57. Markham NR, Zuker M. UNAFold: software for nucleic acid folding and hybridization. Methods Mol Biol. 2008;453:3-31.
58. Qi L, Lucks JB, Liu CC, Mutalik VK, Arkin AP. Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals. Nucleic Acids Res. 2012;40:5775-86.