Finding the common structure shared by two homologous RNAs

Bioinformatics

Volumn 19, Issue 1, 2003, Pages 108-116

  Perriquet, O ^a   Touzet, H ^a   Dauchet, M ^a  

^a ECOLE CENTRALE DE LILLE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

RIBONUCLEASE P; RIBOSOME RNA; RNA 16S; SMALL SUBUNIT RIBOSOMAL RNA; VIRUS RNA;

ARTICLE; BACILLUS; CAMPYLOBACTER; COMPUTER PROGRAM; CONTROLLED STUDY; DESULFOVIBRIO; GENETIC ALGORITHM; HELICOBACTER; INTERMETHOD COMPARISON; METHANOCOCCUS; MULTIGENE FAMILY; NONHUMAN; PREDICTION; PRIORITY JOURNAL; RNA SEQUENCE; RNA STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SULFOLOBUS; UNINDEXED SEQUENCE;

CAMPYLOBACTER; DESULFOVIBRIO; HELICOBACTER; METHANOCOCCUS; RNA VIRUSES; SULFOLOBUS;

EID: 0037252550     PISSN: 13674803     EISSN: None     Source Type: Journal    
DOI: 10.1093/bioinformatics/19.1.108     Document Type: Article

References (21)

1. Brown,J.W. (1999) The Ribonuclease P database. NAR, 27, http://www.mbio.ncsu.edu/RNaseP/.
2. Chen,J.H., Le,S.Y. and Maizel,J.V. (2000) Prediction of common secondary structures of rnas; a genetic algorithm approach. NAR, 28, 991-999.
3. Chiu,D.K.Y. and Kolodziejczak,T. (1991) Inferring consensus structure from nucleic acid sequences. CABIOS, 7, 347-352.
4. Corpet,F. and Michot,B. (1994) RNAlign program: alignment of RNA sequences using both primary and secondary structures. CABIOS, 10, 389-399.
5. Eddy,S.R. and Durbin,R. (1994) RNA sequence analysis using covariance models. NAR, 22, 2079-2088.
6. Gorodkin,J., Heyer,L.J. and Stormo,G.D. (1997) Finding the most significant common sequence and structure motifs in a set of RNA sequences. NAR, 25, 3724-3732.
7. Juan,V. and Wilson,C. (1999) RNA secondary structure prediction based on free energy and phylogenetic analysis. JMB, 289, 935-947.
8. Knudsen,B. and Hein,J. (1999) RNA secondary structure prediction using stochastic context-free grammars and evolutionary history. Bioinformatics, 15, 446-454.
9. Le,S.Y. and Zuker,M. (1990) Common structures of the 5′ non-coding RNA in enteroviruses and rhinoviruses. JMB, 216, 729-741.
10. Mathews,D.H. and Turner,D.H. (2002) Dynalign: an algorithm for finding the secondary structure common to two RNA sequences. JMB, in press.
11. Mathews,D.H., Sabina,J., Zuker,M. and Turner,D.H. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. JMB, 288, 911-940.
12. Mathews,D.H., Turner,D.H. and Zuker,M. (2000) RNA secondary structure prediction. Current Protocols in Nucleic Acid Chemistry, 11, 1-10.
13. Nussinov,R. and Jacobson,A.B. (1980) Fast algorithm for predicting the secondary structure of single stranded RNA. PNAS, 77, 6309-6313.
14. Rivas,E. and Eddy,S.R. (1999) A dynamic programming algorithm for RNA structure prediction including psendoknots. JMB, 285, 2053-2068.
15. Sankoff,D. (1985) Simultaneous solution of the RNA folding, alignment and protosequence problems. SIAM J. Appl. Math., 45, 810-825.
16. Tinoco,I. and Bustamante,C. (1999) How RNA folds JMB. 293, 271-281.
17. Wang,Z. and Zhang,K. (1999) Finding common RNA secondary structures from RNA sequences. Lecture Notes in Computer Science, 1645. pp. 258-269.
18. Witwer,C., Rauscher,S., Hofacker,I.L. and Stadler,P.F. (2001) Conserved RNA secondary structures in picornaviridae, genomes. NAR, 29, 5079-5089.
19. Woese,C.R., Magrum,L.J., Gupta,R., Siegel,R.B., Stahl,D.A., Kop,J., Crawford,N., Brosius,J., Gutell,R., Hogan,J.J. and Noller,H.F. (1980) Secondary structure model for bacterial 168 ribosomal RNA: phylogenetic enzymatic and chemical evidence. NAR, 24:8, 2275-2293. http://www.rna.icmb.utexas.edu/.
20. Wu,M. and Tinoco,I. (1998) RNA folding causes secondary structure rearrangement. PNAS, 95, 11555-11560.
21. Zuker,M. (1989) On finding all suboptimal foldings of an RNA molecule. Science, 244, 48-52.