An Unbiased Adaptive Sampling Algorithm for the Exploration of RNA Mutational Landscapes under Evolutionary Pressure

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 6577 LNBI, Issue , 2011, Pages 501-515

  Waldispühl, Jérôme ^a   Ponty, Yann ^b  

^a MCGILL UNIVERSITY   (Canada)

^b ÉCOLE POLYTECHNIQUE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

EVOLUTIONARY ALGORITHMS; FREE ENERGY; LEARNING ALGORITHMS; MOLECULAR BIOLOGY; POLYNOMIAL APPROXIMATION; RNA;

ADAPTIVE SAMPLING ALGORITHMS; C CONTENTS; FOLDING PROPERTIES; INTERNAL LOOPS; MOLECULAR EVOLUTION; MUTATION PROBABILITY; POLYNOMIAL-TIME; RNA SEQUENCES;

BIOINFORMATICS;

EID: 79953218703     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-20036-6_45     Document Type: Conference Paper

References (35)

1. Cowperthwaite, M., Meyers, L.: How mutational networks shape evolution: Lessons from RNA models. Annual Review of Ecology, Evolution, and Systematics, 203–230 (2008)
2. Halvorsen, M., Martin, J.S., Broadaway, S., Laederach, A.: Disease-associated mutations that alter the RNA structural ensemble. PLoS Genet. 6(8) (2010)
3. Westhof, E.: Toward atomic accuracy in RNA design. Nat. Methods 7(4), 272–273 (2010)
4. Zuker, M., Stiegler, P.: Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 9(1), 133–148 (1981)
5. Parisien, M., Major, F.: The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature 452(7183), 51–55 (2008)
6. McCaskill, J.S.: The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29(6-7), 1105–1119 (1990)
7. Turner, D.H., Mathews, D.H.: NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure. Nucleic Acids Res. 38(Database issue), D280–D282 (2010)
8. Mathews, D.H.: RNA secondary structure analysis using RNAstructure. Curr. Protoc. Bioinformatics ch. 12, Unit 12.6 (2006)
9. Hofacker, I.L.: RNA secondary structure analysis using the vienna RNA package. Curr. Protoc. Bioinformatics ch. 12, Unit12.2 (June 2009)
10. Markham, N.R., Zuker, M.: UNAFold: software for nucleic acid folding and hybridization. Methods Mol. Biol. 453, 3–31 (2008)
11. Grüner, W., Giegerich, R., Strothmann, D., Reidys, C., Weber, J., Hofacker, I., Stadler, P., Schuster, P.: Analysis of RNA sequence structure maps by exhaustive enumeration i. neutral networks. Monatshefte f. Chemie 127(4), 355–374 (1995)
12. Cowperthwaite, M.C., Economo, E.P., Harcombe, W.R., Miller, E.L., Meyers, L.A.: The ascent of the abundant: how mutational networks constrain evolution. PLoS Comput. Biol. 4(7), e1000110 (2008)
13. Stich, M., Lázaro, E., Manrubia, S.C.: Phenotypic effect of mutations in evolving populations of RNA molecules. BMC Evol. Biol. 10, 46 (2010)
14. Schuster, P., Fontana, W., Stadler, P.F., Hofacker, I.L.: From sequences to shapes and back: a case study in RNA secondary structures. Proc. Biol. Sci. 255(1344), 279–284 (1994)
15. Reidys, C., Stadler, P.F., Schuster, P.: Generic properties of combinatory maps: neutral networks of RNA secondary structures. Bull. Math. Biol. 59(2), 339–397 (1997)
16. Waldispühl, J., Devadas, S., Berger, B., Clote, P.: Efficient algorithms for probing the RNA mutation landscape. PLoS Comput. Biol. 4(8), e1000124 (2008)
17. Waldispühl, J., Behzadi, B., Steyaert, J.M.: An approximate matching algorithm for finding (sub-)optimal sequences in S-attributed grammars. Bioinformatics 18 Suppl 2, S250–S259 (2002)
18. Clote, P., Waldispühl, J., Behzadi, B., Steyaert, J.M.: Energy landscape of k-point mutants of an RNA molecule. Bioinformatics 21(22), 4140–4147 (2005)
19. Ding, Y., Lawrence, C.E.: A bayesian statistical algorithm for RNA secondary structure prediction. Comput. Chem. 23(3-4), 387–400 (1999)
20. Chan, C.Y., Carmack, C.S., Long, D.D., Maliyekkel, A., Shao, Y., Roninson, I.B., Ding, Y.: A structural interpretation of the effect of gc-content on effciency of RNA interference. BMC Bioinformatics 10 Suppl 1, S33 (2009)
21. Wang, H.-c., Hickey, D.A.: Evidence for strong selective constraint acting on the nucleotide composition of 16s ribosomal rna genes. Nucleic Acids Res. 30(11), 2501– 2507 (2002)
22. Nussinov, R., Jacobson, A.: Fast algorithm for predicting the secondary structure of single-stranded RNA. Proc. Natl. Acad. Sci. USA 77, 6903–6913 (1980)
23. Waterman, M.S.: Secondary structure of single stranded nucleic acids. Advances in Mathematics Supplementary Studies 1(1), 167–212 (1978)
24. Wuchty, S., Fontana, W., Hofacker, I., Schuster, P.: Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers 49, 145–164 (1999)
25. Denise, A., Ponty, Y., Termier, M.: Controlled non uniform random generation of decomposable structures. Theoretical Computer Science 411(40-42), 3527–3552 (2010)
26. Flajolet, P., Zimmermann, P., Cutsem, B.V.: A calculus for the random generation of labelled combinatorial structures. Theor. Comput. Sci. 132(2), 1–35 (1994)
27. Ponty, Y.: Efficient sampling of RNAsecondary structures from the boltzmann ensemble of low-energy: The boustrophedon method. Journal of Mathematical Biology 56(1-2), 107–127 (2008)
28. Bodini, O., Ponty, Y.: Multi-dimensional boltzmann sampling of languages. DMTCS Proceedings 0(01) (2010)
29. Moments of the boltzmann distribution for rna secondary structures. Bull. Math. Biol. 67(5), 1031–1047 (September 2005)
30. Faugere, J.C.: A new efficient algorithm for computing Gröbner bases (f4). Journal of Pure and Applied Algebra 139(1-3), 61–88 (1999)
31. Gardner, P.P., Daub, J., Tate, J.G., Nawrocki, E.P., Kolbe, D.L., Lindgreen, S., Wilkinson, A.C., Finn, R.D., Griffiths-Jones, S., Eddy, S.R., Bateman, A.: Rfam: updates to the rna families database. Nucleic Acids Res. 37(Database issue), D136– D140 (2009)
32. Djelloul, M., Denise, A.: Automated motif extraction and classification in RNA tertiary structures. RNA 14(12), 2489–2497 (2008)
33. Lemieux, S., Major, F.: RNA canonical and non-canonical base pairing types: a recognition method and complete repertoire. Nucleic Acids Res. 30(19), 4250–4263 (2002)
34. Leontis, N.B., Lescoute, A., Westhof, E.: The building blocks and motifs of RNA architecture. Curr. Opin. Struct. Biol. 16(3), 279–287 (2006)
35. Barash, D., Churkin, A.: Mutational analysis in RNAs: comparing programs for RNA deleterious mutation prediction. Briefings in Bioinformatics (2010)