In article <45jbnu$ff at news.rrz.uni-koeln.de> a1624067 at athena.rrz.Uni-Koeln.DE (Peter Reinert) writes:
> S. Park (separk at pollux.usc.edu) wrote:
> : Hello, I was once told that someone used dynamic programming in order to
> : solve the RNA folding problem. Could anyone tell me where that was
> : published ? Thank you very much for your time.
>> : Regards,
> : Seongbin Park (separk at pollux.usc.edu)
>>> Here are some references:
>> 1. Major, F., Turcotte, M., Gautheret, D., Lapalme, G., Fillion, E., and
> Cedergren, R.
> (1991) Science 253, 1255-1260.
> 2. Major, F., Gautheret, D., and R., C. (1993) Proc. Natl. Acad. Sci.
> (USA) 90, 9408-9412.
> 3. Gautheret, D., Major, F., and Cedergren, R. (1993) J. Mol. Biology
> 229, 1049-1064.
Dynamic programming can be used for prediction of RNA secondary structures.
The articles cited above are concerned with modelling tertiary (3D)
structure using constraint satisfaction and other techniques.
If secondary structures is what you're interested in look at
@Article{Zuker:84,
author = {M. Zuker and D. Sankoff},
title = {{RNA} secondary structures and their prediction},
journal = {Bulletin of Mathematical Biology},
year = {1984},
volume = {46},
number = {4},
pages = {591-621}
}
@Article{Zuker:89,
author = {M. Zuker},
title = {On finding all suboptimal foldings of an {RNA} molecule},
journal = {Science},
year = {1898},
volume = {244},
pages = {48-52}
}
If you want a program that does secondary structure prediction look at:
Zuker's mfold at ftp://snark.wustl.edu/pub
the Vienna RNA package (of which I'm an author) at
ftp://ftp.itc.univie.ac.at/pub/RNA or http://www.tbi.univie.ac.at/~ivo/RNA
Or if you're using a PC get rnadraw from http://mango.mef.ki.se/~ole/rnadraw
Regards,
Ivo Hofacker
--
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| Ivo Hofacker | Theoretical Biophysics |
| | University of Illinois |
| Phone: (217)-244-1855 | 3139 Beckman Institute |
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| Email: ivo at ks.uiuc.edu | 405 N Mathews, Urbana, IL61801 |
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