Have a personal or library account? Click to login
New models and algorithms for RNA pseudoknot order assignment Cover

References

  1. Aalberts, D.P. (2005). Asymmetry in RNA pseudoknots: Observation and theory, Nucleic Acids Research33(7): 2210–2214.10.1093/nar/gki508107996715831794
  2. Adamiak, R., Blazewicz, J., Formanowicz, P., Gdaniec, Z., Kasprzak, M., Popenda, M. and Szachniuk, M. (2004). An algorithm for an automatic NOE pathways analysis in 2D NMR spectra of RNA duplexes, Journal of Computational Biology42(11): 163–180.10.1089/10665270477341694815072694
  3. Adrjanowicz, K., Kaminski, K., Tarnacka, M., Szutkowski, K., Popenda, L., Bartkowiak, G. and Paluch, M. (2016). The effect of hydrogen bonding propensity and enantiomeric composition on the dynamics of supercooled ketoprofen—Dielectric, rheological and NMR studies, Physical Chemistry Chemical Physics18(15): 10585–10593.10.1039/C6CP00578K
  4. Antczak, M., Popenda, M., Zok, T., Sarzynska, J., Ratajczak, T., Tomczyk, K., Adamiak, R.W. and Szachniuk, M. (2016). New functionality of RNAComposer: Application to shape the axis of miR160 precursor structure, Acta Biochimica Polonica63(4): 737–744.10.18388/abp.2016_132927741327
  5. Antczak, M., Popenda, M., Zok, T., Zurkowski, M., Adamiak, R.W. and Szachniuk, M. (2018). New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation, Bioinformatics34(8): 1304–1312.10.1093/bioinformatics/btx783590566029236971
  6. Antczak, M., Zok, T., Popenda, M., Lukasiak, P., Adamiak, R.W., Blazewicz, J. and Szachniuk, M. (2014). RNApdbee—A webserver to derive secondary structures from PDB files of knotted and unknotted RNAs, Nucleic Acids Research42(W1): W368–W372.10.1093/nar/gku330408611224771339
  7. Blazewicz, J., Figlerowicz, M., Kasprzak, M., Nowacka, M. and Rybarczyk, A. (2011). RNA partial degradation problem: Motivation, complexity, algorithm, Journal of Computational Biology18(6): 821–834.10.1089/cmb.2010.015321563977
  8. Blazewicz, J., Frohmberg, W., Gawron, P., Kasprzak, M., Kierzynka, M., Swiercz, A. and Wojciechowski, P. (2013). DNA sequence assembly involving an acyclic graph model, Foundations of Computing and Decision Sciences38(1): 25–34.10.2478/v10209-011-0019-4
  9. Blazewicz, J., Kasprzak, M., Kierzynka, M., Frohmberg, W., Swiercz, A., Wojciechowski, P. and Zurkowski, P. (2018). Graph algorithms for DNA sequencing—Origins, current models and the future, European Journal of Operational Research264(3): 799–812.10.1016/j.ejor.2016.06.043
  10. Blazewicz, J., Szachniuk, M. and Wojtowicz, A. (2005). RNA tertiary structure determination: NOE pathways construction by tabu search, Bioinformatics21(10): 2356–2361.10.1093/bioinformatics/bti35115731205
  11. Bon, M., Micheletti, C. and Orland, H. (2012). McGenus: a Monte Carlo algorithm to predict RNA secondary structures with pseudoknots, Nucleic Acids Research41(3): 1895–1900.10.1093/nar/gks1204356194523248008
  12. Bon, M., Vernizzi, G., Orland, H. and Zee, A. (2008). Topological classification of RNA structures, Journal of Molecular Biology379(4): 900–911.10.1016/j.jmb.2008.04.03318485361
  13. Bron, C. and Kerbosch, J. (1973). Algorithm 457: Finding all cliques of an undirected graph, Communications of the ACM16(9): 575–577.10.1145/362342.362367
  14. Cheng, L., Connor, T.R., Siren, J., Aanensen, D.M. and Corander, J. (2013). Hierarchical and spatially explicit clustering of DNA sequences with BAPS software, Molecular Biology and Evolution30(5): 1224–1228.10.1093/molbev/mst028367073123408797
  15. Chiu, J.K.H. and Chen, Y.-P.P. (2012). Conformational features of topologically classified RNA secondary structures, PLoS ONE7(7): e39907.10.1371/journal.pone.0039907339033022792195
  16. Desai, N., Brown, A.A. and Ramakrishnan, V. (2017). The structure of the yeast mitochondrial ribosome, Science355(6324): 528–531.10.1126/science.aal2415529564328154081
  17. Gan, H.H., Pasquali, S. and Schlick, T. (2003). Exploring the repertoire of RNA secondary motifs using graph theory: Implications for RNA design, Nucleic Acids Research31(11): 2926–2943.10.1093/nar/gkg36515670912771219
  18. Gebert, J., Lätsch, M., Pickl, S.W., Weber, G. and Wünschiers, R. (2006). An algorithm to analyze stability of gene-expression patterns, Discrete Applied Mathematics154(7): 1140–1156.10.1016/j.dam.2004.08.011
  19. Giuliani, A., Krishnan, A., Zbilut, J. and Tomita, M. (2008). Proteins as networks: Usefulness of graph theory in protein science, Current Protein & Peptide Science9(1): 28–38.10.2174/13892030878356570518336321
  20. Kropat, E., Özmen, A., Weber, G., Meyer-Nieberg, S. and Defterli, O. (2016). Fuzzy prediction strategies for gene-environment networks—Fuzzy regression analysis for two-modal regulatory systems, RAIRO Operations Research50(2): 413–435.10.1051/ro/2015044
  21. Kruthika, H.A., Mahindrakar, A.D. and Pasumarthy, R. (2017). Stability analysis of nonlinear time-delayed systems with application to biological models, International Journal of Applied Mathematics and Computer Science27(1): 91–103, DOI: 10.1515/amcs-2017-0007.10.1515/amcs-2017-0007
  22. Kuang, R., Leslie, C.S. and Yang, A.-S. (2004). Protein backbone angle prediction with machine learning approaches, Bioinformatics20(10): 1612–1621.10.1093/bioinformatics/bth13614988121
  23. Kucharík, M., Hofacker, I.L., Stadler, P.F. and Qin, J. (2016). Pseudoknots in RNA folding landscapes, Bioinformatics32(2): 187–194.10.1093/bioinformatics/btv572470810826428288
  24. Kuppusamy, L. and Mahendran, A. (2016). Modelling DNA and RNA secondary structures using matrix insertion–deletion systems, International Journal of Applied Mathematics and Computer Science26(1): 245–258, DOI: 10.1515/amcs-2016-0017.10.1515/amcs-2016-0017
  25. Lai, D., Proctor, J.R., Zhu, J.Y.A. and Meyer, I.M. (2012). R-CHIE: A web server and R package for visualizing RNA secondary structures, Nucleic Acids Research40(12): e95.10.1093/nar/gks241338435022434875
  26. Leontis, N.B. and Zirbel, C.L. (2012). Nonredundant 3D structure datasets for RNA knowledge extraction and benchmarking, in N. Leontis and E. Westhof (Eds), Nucleic Acids and Molecular Biology, Springer Nature, Berlin/Heidelberg, pp. 281–298.10.1007/978-3-642-25740-7_13
  27. Leontis, N. and Westhof, E. (2012). RNA 3D Structure Analysis and Prediction, Springer, Berlin/New York, NY.10.1007/978-3-642-25740-7
  28. Lim, C.S. and Brown, C.M. (2018). Know your enemy: Successful bioinformatic approaches to predict functional RNA structures in viral RNAs, Frontiers in Microbiology8: 2582.10.3389/fmicb.2017.02582575854829354101
  29. Lu, X.-J. and Olson, W.K. (2008). 3DNA: A versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures, Nature Protocols3(7): 1213–1227.10.1038/nprot.2008.104306535418600227
  30. Luby, M. (1986). A simple parallel algorithm for the maximal independent set problem, SIAM Journal on Computing15(4): 1036–1053.10.1137/0215074
  31. Lukasiak, P., Antczak, M., Ratajczak, T., Szachniuk, M., Popenda, M., Adamiak, R.W. and Blazewicz, J. (2015). RNAssess—A web server for quality assessment of RNA 3D structures, Nucleic Acids Research43(W1): W502–W506.10.1093/nar/gkv557448924226068469
  32. Magnus, M., Antczak, M., Zok, T., Wiedemann, J., Lukasiak, P., Cao, Y., Bujnicki, J.M., Westhof, E., Szachniuk, M. and Miao, Z. (2020). RNA-Puzzles toolkit: A computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools, Nucleic Acids Research48(2): 576–588.10.1093/nar/gkz1108714551131799609
  33. Miao, Z. and Westhof, E. (2017). RNA structure: Advances and assessment of 3D structure prediction, Annual Review of Biophysics46: 483–503.10.1146/annurev-biophys-070816-03412528375730
  34. Miskiewicz, J. and Szachniuk, M. (2018). Discovering structural motifs in miRNA precursors from the Viridiplantae kingdom, Molecules23(6): 1367.10.3390/molecules23061367610013529882777
  35. Morimura, H., Tanaka, S.-I., Ishitobi, H., Mikami, T., Kamachi, Y., Kondoh, H. and Inouye, Y. (2013). Nano-analysis of DNA conformation changes induced by transcription factor complex binding using plasmonic nanodimers, ACS Nano7(12): 10733–10740.10.1021/nn403625s24195575
  36. Parisien, M., Cruz, J.A., Westhof, E. and Major, F. (2009). New metrics for comparing and assessing discrepancies between RNA 3D structures and models, RNA15(10): 1875–1885.10.1261/rna.1700409274303819710185
  37. Pasquali, S., Gan, H. and Schlick, T. (2005). Modular RNA architecture revealed by computational analysis of existing pseudoknots and ribosomal RNAs, Nucleic Acids Research33(4): 1384–1398.10.1093/nar/gki26755295515745998
  38. Pillsbury, M., Orland, H. and Zee, A. (2005). Steepest descent calculation of RNA pseudoknots, Physical Review E72(1).10.1103/PhysRevE.72.01191116090005
  39. Popenda, L., Bielecki, L., Gdaniec, Z. and Adamiak, R.W. (2009). Structure and dynamics of adenosine bulged RNA duplex reveals formation of the dinucleotide platform in the C:G-A triple, Arkivoc2009(3): 130–144.10.3998/ark.5550190.0010.311
  40. Popenda, M., Miskiewicz, J., Sarzynska, J., Zok, T. and Szachniuk, M. (2020). Topology-based classification of tetrads and quadruplex structures, Bioinformatics36(4): 1129–1134.10.1093/bioinformatics/btz738703177831588513
  41. Pugalenthi, G., Suganthan, P.N., Sowdhamini, R. and Chakrabarti, S. (2007). SMotif: A server for structural motifs in proteins, Bioinformatics23(5): 637–638.10.1093/bioinformatics/btl67917237055
  42. Purzycka, K., Popenda, M., Szachniuk, M., Antczak, M., Lukasiak, P., Blazewicz, J. and Adamiak, R. (2015). Automated 3D RNA structure prediction using the RNAComposer method for riboswitches, in S.J. Chen and D.H. Burke Aguero (Eds), Methods in Enzymology, Vol. 553, Elsevier, San Diego, CA, pp. 3–34.
  43. Radom, M., Rybarczyk, A., Szawulak, B., Andrzejewski, H., Chabelski, P., Kozak, A. and Formanowicz, P. (2017). Holmes: A graphical tool for development, simulation and analysis of Petri net based models of complex biological systems, Bioinformatics33(23): 3822–3823.10.1093/bioinformatics/btx49228961696
  44. Rebis, T., Lijewski, S., Nowicka, J., Popenda, L., Sobotta, L., Jurga, S., Mielcarek, J., Milczarek, G. and Goslinski, T. (2015). Electrochemical properties of metallated porphyrazines possessing isophthaloxybutylsulfanyl substituents: Application in the electrocatalytic oxidation of hydrazine, Electrochimica Acta168: 216–224.10.1016/j.electacta.2015.03.191
  45. Reidys, C.M., Huang, F.W.D., Andersen, J.E., Penner, R.C., Stadler, P.F. and Nebel, M.E. (2011). Topology and prediction of RNA pseudoknots, Bioinformatics27(8): 1076–1085.10.1093/bioinformatics/btr09021335320
  46. Rietveld, K., Poelgeest, R.V., Pleij, C., Boom, J.V. and Bosch, L. (1982). The tRNA-like structure at the 3' terminus of turnip yellow mosaic virus RNA. Differences and similarities with canonical tRNA, Nucleic Acids Research10(6): 1929–1946.
  47. Rødland, E.A. (2006). Pseudoknots in RNA secondary structures: Representation, enumeration, and prevalence, Journal of Computational Biology13(6): 1197–1213.10.1089/cmb.2006.13.119716901237
  48. Rybarczyk, A., Hertz, A., Kasprzak, M. and Blazewicz, J. (2017). Tabu search for the RNA partial degradation problem, International Journal of Applied Mathematics and Computer Science27(2): 401–415, DOI: 10.1515/amcs-2017-0028.10.1515/amcs-2017-0028
  49. Saenger, W. (1984). Principles of Nucleic Acid Structure, Springer-Verlag, London.10.1007/978-1-4612-5190-3
  50. Sarzynska, J. and Kulinski, T. (2005). Dynamics and stability of GCAA tetraloops with 2-aminopurine and purine substitutions, Journal of Biomolecular Structure and Dynamics22(4): 425–439.10.1080/07391102.2005.1050701415588106
  51. Schlick, T. (2018). Adventures with RNA graphs, Methods143: 16–33.10.1016/j.ymeth.2018.03.009605191829621619
  52. Seetin, M. and Mathews, D. (2011). Automated RNA tertiary structure prediction from secondary structure and low-resolution restraints, Journal of Computational Chemistry32(10): 2232–2244.10.1002/jcc.21806328833421509787
  53. Shi, Y.-Z., Jin, L., Feng, C.-J., Tan, Y.-L. and Tan, Z.-J. (2018). Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions, PLOS Computational Biology14(6): e1006222.10.1371/journal.pcbi.1006222600793429879103
  54. Simon, M. (2005). Emergent Computation. Emphasizing Bioinformatics, Springer New York, New York, NY.10.1007/b138851
  55. Slabinski, L., Jaroszewski, L., Rodrigues, A.P., Rychlewski, L., Wilson, I.A., Lesley, S.A. and Godzik, A. (2007). The challenge of protein structure determination-lessons from structural genomics, Protein Science16(11): 2472–2482.10.1110/ps.073037907221168717962404
  56. Staple, D.W. and Butcher, S.E. (2005). Pseudoknots: RNA structures with diverse functions, PLoS Biology3(6): e213.10.1371/journal.pbio.0030213114949315941360
  57. Sun, T.-t., Zhao, C. and Chen, S.-J. (2018). Predicting cotranscriptional folding kinetics for riboswitch, The Journal of Physical Chemistry B122(30): 7484–7496.10.1021/acs.jpcb.8b04249634527729985608
  58. Szachniuk, M. (2019). RNApolis: Computational platform for RNA structure analysis, Foundations of Computing and Decision Sciences44(2): 241–257.10.2478/fcds-2019-0012
  59. Szachniuk, M., Cola, M.C.D., Felici, G. and Blazewicz, J. (2014). The orderly colored longest path problem—A survey of applications and new algorithms, RAIRO—Operations Research48(1): 25–51.10.1051/ro/2013046
  60. Szachniuk, M., Cola, M.C.D., Felici, G., de Werra, D. and Blazewicz, J. (2015). Optimal pathway reconstruction on 3D NMR maps, Discrete Applied Mathematics182: 134–149.10.1016/j.dam.2014.04.010
  61. Szostak, N., Royo, F., Rybarczyk, A., Szachniuk, M., Blazewicz, J., del Sol, A. and Falcon-Perez, J.M. (2014). Sorting signal targeting mRNA into hepatic extracellular vesicles, RNA Biology11(7): 836–844.10.4161/rna.29305417995824921245
  62. Tarjan, R.E. and Trojanowski, A.E. (1977). Finding a maximum independent set, SIAM Journal on Computing6(3): 537–546.10.1137/0206038
  63. Vernizzi, G., Orland, H. and Zee, A. (2016). Classification and predictions of RNA pseudoknots based on topological invariants, Physical Review E94(4).10.1103/PhysRevE.94.04241027841638
  64. Weber, G., Defterli, O., Gök, S.Z.A. and Kropat, E. (2011). Modeling, inference and optimization of regulatory networks based on time series data, European Journal of Operational Research211(1): 1–14.10.1016/j.ejor.2010.06.038
  65. Weber, G., Kropat, E., Akteke-Öztürk, B. and Görgülü, Z. (2009). A survey on OR and mathematical methods applied on gene-environment networks, CEJOR17(3): 315–341.10.1007/s10100-009-0092-4
  66. Wiedemann, J. and Milostan, M. (2017). StructAnalyzer—A tool for sequence vs. structure similarity analysis, Acta Biochimica Polonica63(4): 753–757.
  67. Wiedemann, J., Zok, T., Milostan, M. and Szachniuk, M. (2017). LCS-TA to identify similar fragments in RNA 3D structures, BMC Bioinformatics18(1): 456.10.1186/s12859-017-1867-6565159829058576
  68. Wojciechowski, P., Frohmberg, W., Kierzynka, M., Zurkowski, P. and Blazewicz, J. (2016). G-MAPSEQ—A new method for mapping reads to a reference genome, Foundations of Computing and Decision Sciences41(2): 123–142.10.1515/fcds-2016-0007
  69. Zemla, A. (2003). LGA: A method for finding 3D similarities in protein structures, Nucleic Acids Research31(13): 3370–3374.10.1093/nar/gkg57116897712824330
  70. Zok, T., Antczak, M., Riedel, M., Nebel, D., Villmann, T., Lukasiak, P., Blazewicz, J. and Szachniuk, M. (2015). Building the library of RNA 3D nucleotide conformations using the clustering approach, International Journal of Applied Mathematics and Computer Science25(3): 689–700, DOI: 10.1515/amcs-2015-0050.10.1515/amcs-2015-0050
  71. Zok, T., Antczak, M., Zurkowski, M., Popenda, M., Blazewicz, J., Adamiak, R.W. and Szachniuk, M. (2018). RNApdbee 2.0: Multifunctional tool for RNA structure annotation, Nucleic Acids Research46(W1): W30–W35.
DOI: https://doi.org/10.34768/amcs-2020-0024 | Journal eISSN: 2083-8492 | Journal ISSN: 1641-876X
Language: English
Page range: 315 - 324
Submitted on: Jul 25, 2019
Accepted on: Mar 12, 2020
Published on: Jul 4, 2020
Published by: University of Zielona Góra
In partnership with: Paradigm Publishing Services
Publication frequency: 4 issues per year

© 2020 Tomasz Zok, Jan Badura, Sylwester Swat, Kacper Figurski, Mariusz Popenda, Maciej Antczak, published by University of Zielona Góra
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.