Determinants of simulated RNA evolution

Journal of Theoretical Biology

Volumn 238, Issue 3, 2006, Pages 726-735

  Kupczok, Anne ^a   Dittrich, Peter ^a  

^a FRIEDRICH SCHILLER UNIVERSITY JENA   (Germany)

Author keywords

Divergence threshold; Error threshold; Local sequence structure alignment; RNA evolution

Indexed keywords

RNA;

RNA;

ARTICLE; MATHEMATICAL ANALYSIS; MOLECULAR EVOLUTION; MOLECULAR MODEL; MUTATION RATE; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; QUALITATIVE ANALYSIS; SIMULATION;

ANIMALS; BIOGENESIS; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; MODELS, GENETIC; MUTATION; NUCLEIC ACID CONFORMATION; RNA; SELECTION (GENETICS); SEQUENCE ALIGNMENT;

EID: 30444449304     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2005.06.019     Document Type: Article

References (18)

1. R. Backofen, and S. Will Local sequence-structure motifs in RNA J. Bioinformat. Comput. Biol. 2 4 2004 681 698
2. P. Beldade, K. Koops, and P.M. Brakefield Modularity, individuality, and evo-devo in butterfly wings Proc. Natl Acad. Sci. USA 99 22 2002 14262 14267
3. M. Eigen, and P. Schuster The hypercycle: a principle of natural self-organisation part A Naturwissenschaften 64 11 1977 541 565
4. W. Fontana, and P. Schuster Continuity in evolution: on the nature of transitions Science 280 1998 1451 1455
5. W. Fontana, D.A.M. Konings, P.F. Stadler, and P. Schuster Statistics of RNA secondary structures Biopolymers 33 9 1993 1389 1404
6. W. Fontana, P.F. Stadler, E.G. Bornberg-Bauer, T. Griesmacher, I.L. Hofacker, M. Tacker, P. Tarazona, E. Weinberger, and P. Schuster Rna folding and combinatory landscapes Phys. Rev. E 47 3 1993 2083 2099
7. I. Hofacker, W. Fontana, P. Stadler, S. Bonhoeffer, M. Tacker, and P. Schuster Fast folding and comparison of RNA secondary structures Monatsh. Chem. 125 1994 167 188
8. W.A. Huynen, P.F. Stadler, and W. Fontana Smoothness within ruggedness: the role of neutrality in adaption Proc. Natl Acad. Sci. USA 93 1 1996 397 401
9. D.H. Mathews, J. Sabina, M. Zuker, and D.H. Turner Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure J. Mol. Biol. 288 5 1999 911 940
10. J.S. McCaskill The equilibrium partition function and base pair binding probabilities for RNA secondary structures Biopolymers 29 6-7 1990 1105 1119
11. M. Nowak, and P. Schuster Error thresholds of replication in finite populations mutation frequencies and the onset of muller's ratchett J. Theor. Biol. 137 1989 375 395
12. C. Reidys, C. Forst, and P. Schuster Replication and mutation on neutral networks Bull. Math. Biol. 63 1 2001 57 94
13. P. Schuster Evolution in silico and in vitro: the RNA model Biol. Chem. 382 9 2001 1301 1314
14. B.A. Shapiro An algorithm for comparing multiple RNA secondary structures Comput. Appl. Biosci. 4 3 1988 387 393
15. B.A. Shapiro, and K. Zhang Comparing multiple RNA secondary structures using tree comparisons Comput. Appl. Biosci. 6 4 1990 309 318
16. N. Takeuchi, P.H. Poorthuis, and P. Hogeweg Phenotypic error threshold; additivity and epistasis in RNA evolution BMC Evol. Biol. 5 9 2005
17. C.O. Wilke, R.E. Lenski, and C. Adami Compensatory mutations cause excess of antagonistic epistasis in RNA secondary structure folding BMC Evol. Biol. 3 3 2003
18. M. Zuker, and P. Stiegler Optimal computer folding of large RNA sequences using thermodynamic and auxiliary information Nucl. Acid. Res. 9 1 1981 133 148