CentroidFold: A web server for RNA secondary structure prediction

Nucleic Acids Research

Volumn 37, Issue SUPPL. 2, 2009, Pages

  Sato, Kengo ^a,b   Hamada, Michiaki ^b,c   Asai, Kiyoshi ^b,d   Mituyama, Toutai ^b  

^a Koto ku   (Japan)

^b NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^c MIZUHO INFORMATION AND RESEARCH INSTITUTE   (Japan)

^d UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

ACCURACY; ALGORITHM; ARTICLE; BASE PAIRING; CLIENT SERVER APPLICATION; MATHEMATICAL ANALYSIS; PREDICTION; PRIORITY JOURNAL; RNA SECONDARY STRUCTURE; RNA SEQUENCE; RNA STRUCTURE; SEARCH ENGINE; SEQUENCE ALIGNMENT; WEB BROWSER;

ALGORITHMS; COMPUTER GRAPHICS; INTERNET; NUCLEIC ACID CONFORMATION; RNA, TRANSFER; RNA, UNTRANSLATED; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 67849086863     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp367     Document Type: Article

References (11)

1. Zuker,M. and Stiegler,P. (1981) Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res., 9, 133-148.
2. Hofacker,I.L. (2003) Vienna RNA secondary structure server. Nucleic Acids Res., 31, 3429-3431.
3. Dowell,R.D. and Eddy,S.R. (2004) Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction. BMC Bioinformatics, 5, 71.
4. Durbin,R., Eddy,S., Krogh,A. and Mitchison,G. (1998) Biological Sequence Analysis. Cambridge University Press, Cambridge, England.
5. Knudsen,B. and Hein,J. (2003) Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res., 31 3423-3428.
6. Ding,Y. and Lawrence,C.E. (2003) A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Res., 31, 7280-7301.
7. Ding,Y., Chan,C.Y. and Lawrence,C.E. (2005) RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. RNA, 11, 1157-1166.
8. Carvalho,L.E. and Lawrence,C.E. (2008) Centroid estimation in discrete high-dimensional spaces with applications in biology. Proc. Natl Acad. Sci. USA, 105, 3209-3214.
9. Do,C.B., Woods,D.A. and Batzoglou,S. (2006) CONTRAfold: RNA secondary structure prediction without physics-based models. Bioinformatics, 22, e90-e98.
10. Hamada,M., Kiryu,H., Sato,K., Mituyama,T. and Asai,K. (2009) Prediction of RNA secondary structure using generalized centroid estimators. Bioinformatics, 25, 465-473.
11. McCaskill,J.S. (1990) The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers, 29, 1105-1119.