RNA folding programs

ROOSSINCK,MARILYN roossinck at aardvark.ucs.uoknor.edu
Mon Dec 5 15:14:00 EST 1994

In article <Pine.3.88.9412011754.A11032-0100000 at server>, gottlieb at SERVER.NYBC.ORG (Paul Gottlieb) writes...
>	I am interested in identifying pseudoknot structures in 
>transcripts. Does anyone know about RNA folding programs that are capable 
>of finding these structures. Thanks in advance for any information.

The "STAR" program "Structure Analysis of RNA" can predict pseudoknots,
and also is the only folding program that has ever accurately predicted a known
secondary structure.  (NAR 18:3035-3044).  It uses a different algorithm from
the Zuker based programs.  Although it is a bit user unfriendly (the latest
version isn't too bad) it is a very useful program.  It is available from:
	F.H.D. van Batenburg
	Bio-informatika of the Institute of Theoretical Biology
	Leiden University
	Kaiserstraat 63, 2311GP Leiden
	The Netherlands
It is not a free program--write for current cost.

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