Cofolga: A genetic algorithm for finding the common folding of two RNAs

Computational Biology and Chemistry

Volumn 29, Issue 2, 2005, Pages 111-119

  Taneda, Akito ^a  

^a HIROSAKI UNIVERSITY   (Japan)

Author keywords

Covariation; Free energy minimization; Secondary structure prediction; Sequence alignment; Simulated annealing

Indexed keywords

FINITE ELEMENT METHOD; FREE ENERGY; FUNCTIONS; GENES; GENETIC ALGORITHMS; ITERATIVE METHODS; MOLECULAR ORIENTATION; MUTAGENESIS; SIMULATED ANNEALING;

COVARIATION; FREE ENERGY MINIMIZATION; SECONDARY STRUCTURE PREDICTION; SEQUENCE ALIGNMENT;

RNA;

RIBONUCLEASE P; RNA 5S; SIGNAL RECOGNITION PARTICLE; SRP14 PROTEIN, HUMAN; TRANSFER RNA;

ALGORITHM; ARTICLE; CHEMISTRY; COMPARATIVE STUDY; CONFORMATION; GENETICS; HUMAN; MOLECULAR GENETICS; SEQUENCE HOMOLOGY; THERMODYNAMICS;

ALGORITHMS; HUMANS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RIBONUCLEASE P; RNA, RIBOSOMAL, 5S; RNA, TRANSFER; SEQUENCE HOMOLOGY, NUCLEIC ACID; SIGNAL RECOGNITION PARTICLE; THERMODYNAMICS;

EID: 16344370402     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2005.02.004     Document Type: Article

References (20)

1. J.W. Brown The ribonuclease P database Nucleic Acids Res. 27 1999 314
2. J.H. Chen, S.Y. Le, and J.V. Maizel Prediction of common secondary structures of RNAs: a genetic algorithm approach Nucleic Acids Res. 28 2000 991 999
3. D.K.Y. Chiu, and T. Kolodziejczak Inferring consensus structure from nucleic acid sequences Comput. Appl. Biosci. 7 1991 347 352
4. M. Gerstein, and M. Levitt Using iterative dynamic programming to obtain accurate pairwise and multiple alignments of protein structures Proc. Int. Conf. Intell. Syst. Mol. Biol. 4 1996 59 67
5. D.E. Goldberg Genetic Algorithms in Search, Optimization and Machine Learning 1987 Addison-Wesley NewYork
6. J. Gorodkin, L.J. Heyer, and G.D. Stormo Finding the most significant common sequence and structure motifs in a set of RNA sequences Nucleic Acids Res. 25 1997 3724 3732
7. R.R. Gutell, A. Power, G.Z. Hertz, E.J. Putz, and G.D. Stormo Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods Nucleic Acids Res. 20 1992 5785 5795
8. I.L. Hofacker, M. Fekete, and P.F. Stadler Secondary structure prediction for aligned RNA sequences J. Mol. Biol. 319 2002 1059 1066
9. V. Juan, and C. Wilson RNA secondary structure prediction based on free energy and phylogenetic analysis J. Mol. Biol. 289 1999 935 947
10. S. Kirkpatrick, C.D. Gelatt, and M.P. Vecchi Jr. Optimization by simulated annealing Science 220 1983 671 680
11. D.H. Mathews, and D.H. Turner Dynalign: an algorithm for finding the secondary structure common to two RNA sequences J. Mol. Biol. 317 2002 191 203
12. 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 1999 911 940
13. C. Notredame, E.A. O'Brien, and D.G. Higgins RAGA: RNA sequence alignment by genetic algorithm Nucleic Acids Res. 25 1997 4570 4580
14. O. Perriquet, H. Touzet, and M. Dauchet Finding the common structure shared by two homologous RNAs Bioinformatics 19 2003 108 116
15. M.A. Rosenblad, J. Gorodkin, B. Knudsen, C. Zwieb, and T. Samuelsson SRPDB (signal recognition particle database) Nucleic Acids Res. 31 2003 363 364
16. D. Sankoff Simultaneous solution of the RNA folding, alignment and protosequence problems SIAM J. Appl. Math. 45 1985 810 824
17. M. Schmitz, and G. Steger Description of RNA folding by "simulated annealing" J. Mol. Biol. 255 1996 254 266
18. M. Sprinzl, C. Horn, M. Brown, A. Ioudovitch, and S. Steinberg Compilation of tRNA sequences and sequences of tRNA genes Nucleic Acids Res. 26 1998 148 153
19. M. Szymanski, M.Z. Barciszewska, V.A. Erdmann, and J. Barciszewski 5S Ribosomal RNA Database Nucleic Acids Res. 30 2002 176 178
20. Zuker, M., 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31, 3406-3415 (quick fold server and free-energy parameters are available at http://www.bioinfo.rpi.edu/ ∼zukerm/).