RNA Movies 2: Sequential animation of RNA secondary structures

Nucleic Acids Research

Volumn 35, Issue SUPPL.2, 2007, Pages

  Kaiser, Alexander ^a   Krüger, Jan ^a   Evers, Dirk J ^a  

^a BIELEFELD UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; RNA;

ALGORITHM; ARTICLE; BIOLOGY; CHEMISTRY; COMPUTER INTERFACE; COMPUTER LANGUAGE; COMPUTER SIMULATION; CONFORMATION; GENETICS; INFORMATION PROCESSING; INTERNET; METHODOLOGY; MULTIMEDIA; NATRONOBACTERIUM;

ALGORITHMS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DATA DISPLAY; INTERNET; MULTIMEDIA; NATRONOBACTERIUM; NUCLEIC ACID CONFORMATION; PROGRAMMING LANGUAGES; RNA; RNA, BACTERIAL; USER-COMPUTER INTERFACE;

EID: 34547593472     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm309     Document Type: Article

References (11)

1. Mathews, D.H. and Turner, D.H. (2006) Prediction of RNA secondary structure by free energy minimization. Curr. Opin. Struct. Biol., 16, 270-278.
2. Flamm, C., Hofacker, I.L., Maurer-Stroh, S., Stadler, P.F. and Zehl, M. (2001) Design of multistable RNA molecules. RNA, 7, 254-265.
3. Gultyaev, A.P. (1991) The computer simulation of RNA folding involving pseudoknot formation. Nucleic Acids Res., 19, 2489-2494.
4. Isambert, H. and Siggia, E. (2000) Modeling RNA folding paths with pseudoknots: application to hepatitis delta virus ribozyme. Proc. Natl Acad. Sci. USA, 97, 6515-6520.
5. Mironov, A.A., Dyakonovo, L.P. and Kister, A.E. (1985) A kinetic approach to the prediction of RNA secondary structures. J. Biomol. Struct. Dynam., 2, 953-962.
6. Steffen, P., Voß, B., Rehmsmeier, M., Reeder, J. and Giegerich, R. (2006) RNAshapes: an integrated RNA analysis package based on abstract shapes. Bioinformatics, 22, 500-503.
7. Evers, D.J. and Giegerich, R. (1999) RNA Movies: visualizing RNA secondary structure spaces. Bioinformatics, 15, 32-37.
8. Bruccoleri, R.E. and Heinrich, G. (1988) An improved algorithm for nucleic acid secondary structure display. Comput. Appl. Biosci., 4, 167-173.
9. De Rijk, P. and De Wachter, R. (1993) DCSE, an interactive tool for sequence alignment and secondary structure search. Comput. Appl. Biosci., 9, 735-740.
10. Seibel, P.N., Kruger, J., Hartmeier, S., Schwarzer, K., Loewenthal, K., Mersch, H., Dandekar, T. and Giegerich, R. (2006) XML schemas for common bioinformatic data types and their application in workflow systems. BMC Bioinformatics, 7, 490.
11. Reeder, J. and Giegerich, R. (2004) Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. BMC Bioinformatics, 5, 104.