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Pseudoknots Prediction on RNA Secondary Structure Using Term Rewriting

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Bioinformatics and Biomedical Engineering (IWBBIO 2015)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 9043))

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Abstract

The presences of Pseudoknots generate computational complexities during RNA (Ribonucleic Acid) secondary structure analysis. It is a well known NP hard problem in computational system. It is very essential to have an automated algorithm based system to predict the Pseudoknots from billions of data set. RNA plays a vital role in meditation of cellular information transfer from genes to functional proteins. Pseudoknots are seldom repeated forms that produce misleading computational cost and memory. Memory reducing under bloom filter proposes a memory efficient algorithm for prediction Pseudoknot of RNA secondary structure. RNA Pseudoknot structure prediction based on bloom filter rather than dynamic programming and context free grammar. At first, Structure Rewriting (SR) technique is used to represent secondary structure. Secondary structure is represented in dot bracket representation. Represented secondary structure is separated into two portions to reduce structural complexity. Dot bracket is placed into bloom filter for finding Pseudoknot. In bloom filter, hashing table is used to occupy the RNA based nucleotide. Our proposed algorithm experiences on 105 Pseudoknots in pseudobase and achieves accuracy 66.159% to determine structure.

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References

  1. Batey, R.T., Rambo, R.P., Doudna, J.: Tertiary Motifs in RNA Structure and Folding. Angew. Chem. Int. Ed. Engl. 38(16), 2326–2343 (1999)

    Article  Google Scholar 

  2. He, S., Liu, C., Skogerbo, G., Zhao, H., Wang, J., Liu, T., Bai, B., Zhao, Y., Chen, R.: Noncode v2.0: Decoding the Non-Coding. Nucleic Acids Research 36(Database), D170–D172 (2007)

    Google Scholar 

  3. Griffiths-Jones, S., Bateman, A., Marshall, M., Khanna, A., Eddy, S.R.: Rfam: An RNA Family Database. Nucleic Acids Research 31(1), 439–441 (2003)

    Article  Google Scholar 

  4. Le, S.Y., Chen, J.H., Maizel, J.: Structure and Methods: Human Genome Initiative and DNA Recombination. Chapter Efficient Searches for Unusual Folding Regions in RNA Sequences 1, 127–130 (1990)

    Google Scholar 

  5. Rivas, E., Eddy, S.: Secondary Structure Alone is Generally Not Statisti-cally Significant for the Detection of Noncoding RNAs. Bioinformatics 16(7), 583–605 (2000)

    Article  Google Scholar 

  6. Thomas, K.F., Wong, Y.S., Chiu, T.W., Lam, S.M.: Memory Efficient Algorithms for Structural Alignment of RNAs with Pseudoknots. IEEE/ACM Transactions on Computational Biology and Bioinformatics 9(1), 161–168 (2012)

    Article  Google Scholar 

  7. Hofacker, I.L., Bernhart, S.H.F., Stadler, P.F.: Alignment of RNA base pairing probability matrices. Bioinformatics 20(14), 2222–2227 (2004)

    Article  Google Scholar 

  8. Lee, D., Han, K.: Prediction of RNA Pseudoknots – Comparative Study of Genetic Algorithms. Genome Informatics 13, 414–415 (2003)

    Google Scholar 

  9. Staple, D.W., Butcher, S.E.: Pseudoknots: RNA Structures with Diverse Functions. PLoS Biology 3(6), e213 (2005)

    Google Scholar 

  10. Pley, H.W., Flaherty, K.M., McKay, D.B.: Threedimensional structure of a hammerhead ribozyme. Nature 372, 68–74 (1994)

    Google Scholar 

  11. Sankoff, D.: Simultaneous Solution of the RNA Folding, Alignment and Protosequence Problems. SIAM Journal on Applied Mathematics 45(5), 810–825 (1985)

    Article  MATH  MathSciNet  Google Scholar 

  12. Dowell, R.D., Eddy, S.R.: Efficient pair wise RNA structure prediction and alignment using sequence alignment constraints. BMC Bioinformatics 7(400) (2006)

    Google Scholar 

  13. Holmes, I.: Accelerated probabilistic inference of rna structure evolution. BMC Bioinformatics 6(1), 73 (2005)

    Article  Google Scholar 

  14. Knudsen, B., Hein, J.: Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res. 31(13), 3423–3428 (2003)

    Article  Google Scholar 

  15. Thompson, J.D., Higgins, D.G., Gibson, T.J.: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22(22), 4673–4680 (1994)

    Article  Google Scholar 

  16. Blanchette, M., Kent, W.J., Riemer, C., Elnitski, L., Smit, A.F., Roskin, K.M., Baertsch, R., Rosenbloom, K., Clawson, H., Green, E.D., Haussler, D., Miller, W.: Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 14(4), 708–715 (2004)

    Article  Google Scholar 

  17. Mccaskill, S.: The equilibrium partition function and base pair binding probabilities for rna secondarystructure. Biopolymers 29(6-7), 1105–1119 (1990)

    Article  Google Scholar 

  18. Torarinsson, E., Havgaard, J.H., Gorodkin, J.: Multiple structural align-ment and clustering of RNA sequences. Bioinformatics 23(8), 926–932 (2007)

    Article  Google Scholar 

  19. Washietl, S., Hofacker, I.L., Stadler, P.F.: Fast and reliable prediction of noncoding RNAs. Proc. Natl. Acad. Sci. U S A 102(7), 2454–2459 (2005)

    Article  Google Scholar 

  20. Hochsmann, M., Voss, B., Giegerich, R.: Pure multiple RNA secondary structure alignments: a progressive profile approach. IEEE/ACM Trans. Comput. Biol. Bioinform. 1(1), 53–62 (2004)

    Article  Google Scholar 

  21. Touzet, H., Perriquet, O.: CARNAC:folding families of related RNAs. Nucl. Acids Res. 32(suppl. 2), W142–W145 (2004)

    Google Scholar 

  22. Bloom, B.: Space/time Trade-offs in Hash Coding with Allowable Errors. Communications of the ACM 13(7), 422–426

    Google Scholar 

  23. Eker, S.: Fast matching in combination of regular equational theories. In: Meseguer, J. (ed.) Proceedings First International Workshop on Rewriting Logic and its Applications. Electronic Notes in Theoretical Computer Science, vol. 4, pp. 90–109. Elsevier (1996)

    Google Scholar 

  24. Zuker, M.: Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research 31(13), 3406–3415 (2003)

    Article  Google Scholar 

  25. Rouzina, I., Bloomfield, V.A.: Heat Capacity Effects on the Melting of DNA.2. Analysis of Nearest-Neighbor Base Pair Effects. Biophysical Journal 77(6), 3252–3255 (1999)

    Google Scholar 

  26. Bloom, B.H.: Space/time trade-offs in hash coding with allowable errors. Communications of the ACM 13(7), 422–426 (1970)

    Article  MATH  Google Scholar 

  27. Tabaska, J., Cary, R., Gabow, H., Stormo, G.: An RNA folding method capable of identifying pseudoknots and base triples. Bioinformatics 14(8), 691–699 (1998)

    Article  Google Scholar 

  28. Ruan, J., Stormo, G.D., Zhang, W.: An Iterated loop matching approach to the prediction of RNA secondary structures with Pseudoknots. Bioinformatics 20(1), 58–66 (2004)

    Article  Google Scholar 

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Authors and Affiliations

  1. Department of Computer Science and Engineering, Chittagong University of Engineering and Technology, Cuet Road, Zip Code-4349, Bangladesh

    Linkon Chowdhury & Mohammad Ibrahim Khan

Authors
  1. Linkon Chowdhury
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  2. Mohammad Ibrahim Khan
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Editor information

Editors and Affiliations

  1. Dpto. de Arquitectura y Tecnología de Computadores (ATC)., E.T.S. de Ingenierías en Informática y Telecomunicación. CITIC-UGR, Universidad de Granada, c/ Periodista Daniel Saucedo Aranda s/n, 18071, Granada, Spain

    Francisco Ortuño

  2. E.T.S. Ingenierías Informática y de Telecomunicación , , Dpto. Arquitectura y Tecnología de Computadores, CITIC-UGR, Universidad de Granada, C Periodista Rafael Gómez Montero, 18071, Granada, Spain

    Ignacio Rojas

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Chowdhury, L., Khan, M.I. (2015). Pseudoknots Prediction on RNA Secondary Structure Using Term Rewriting. In: Ortuño, F., Rojas, I. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2015. Lecture Notes in Computer Science(), vol 9043. Springer, Cham. https://doi.org/10.1007/978-3-319-16483-0_56

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  • DOI: https://doi.org/10.1007/978-3-319-16483-0_56

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-16482-3

  • Online ISBN: 978-3-319-16483-0

  • eBook Packages: Computer ScienceComputer Science (R0)

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