Toward turbo decoding of RNA secondary structure

ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings

Volumn 1, Issue , 2007, Pages

  Harmanci, A Ozgun ^a   Sharma, Gaurav ^a,b   Mathews, David H ^b  

^a University of Rochester   (United States)

^b UNIVERSITY OF ROCHESTER MEDICAL CENTER   (United States)

Author keywords

Iterative probabilistic decoding; Pairwise alignment; RNA; Secondary structure; Structural alignment

Indexed keywords

ALGORITHMS; DIGITAL COMMUNICATION SYSTEMS; ITERATIVE METHODS; PROBABILISTIC LOGICS; TURBO CODES;

ITERATIVE PROBABILISTIC DECODING; PAIRWISE ALIGNMENT; RNA SECONDARY STRUCTURE; STRUCTURAL ALIGNMENT;

RNA;

EID: 34248674030     PISSN: 15206149     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ICASSP.2007.366692     Document Type: Conference Paper

References (15)

1. J. D. Watson, T. A. Baker, S. P. Bell, A. Gann, M. Levine, and R. Losick, Molecular Biology of the Gene, 5th ed. San Franciso, CA: Pearson Education, Benjamin Cummings, 2004.
2. I. Tinoco, Jr. and C. Bustamante, "How RNA folds," J Mol Biol., vol. 293, no. 2, pp. 271-281, 1999.
3. R. Durbin, S. Eddy, A. Krogh, and G. Mitchison, Biological Sequence Analysis : Probabilistic Models of Proteins and Nucleic Acids. Cambridge, UK: Cambridge University Press, 1999.
4. B. Masoumi and M. Turcotte, "Simultaneous alignment and structure prediction of three RNA sequences," Int J Bioinformatics Research and Applications, vol, 1, pp. 230-245, 2005.
5. D. H. Mathews and D. H. Turner, "Dynalign: An algorithm for finding the secondary structure common to two RNA sequences," Journal of Molecular Biology, vol. 317, pp. 191-203, 2002.
6. R. D. Dowell and S. R. Eddy, "Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure pcediction," BMC Bioinformatics, vol. 5, no. 1, p. 71, 2004.
7. I. Holmes, "Accelerated probabilistic inference of RNA structure evolution," BMC Bioinformatics, vol. 6, no. 1, p. 73, March 2005.
8. D. Sankoff, "Simultaneous solution of RNA folding, alignment and protosequenee problems," SIAM Journal of Applied Mathematics, vol. 45, no, 5, pp, 810-825, Oct. 1985.
9. A. V. Uzilov, J. M. Keegan, and D. H. Mathews, "Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change," BMC Bioinformatics, vol. 7, no. 1, p. 173, 2006.
10. L. R. Rabiner and B. H. Juang, "An introduction, to hidden markov models," ASSPMAG, vol. 3, no. 1,: pp. 4-16, Jan. 1986.
11. A. Harmanci, G. Sharma, and D. Mathews, "Efficient, pairwise RNA structure prediction using probabilistic alignment constraints in dynalign," BMC Bioinformatics, vol. 4, 2006, submitted for review Sept. 2006.
12. D. H. Mathews, "Predicting a set of minimal free energy RNA secondary structures common to two sequences,"Bioinformatics, vol. 21, no. 10, pp. 2246-2253, May 2005.
13. M. Zuker, "Computer prediction of RNA structure "Methods in Enzymology, vol. 180, pp. 262-288, 1989.
14. M. Szymanski, M. Z. Barciszewska, J. Barciszewski, and V. A. Erdmann, "5S ribosomal RNA database Y2K," Nucleic Acids Research, vol. 28, pp. 166-167, 2000.
15. M. Sprinzl, C. Hurn, M. Brown, A. Ioudovitch, and S. Steinberg, "Compilation of tRNA sequences and sequences of tRNA genes," Nucleic Acids Research, vol. 26, pp. 148-153, 1998.