RNA, inverted sequences, & structure?

Peter Gegenheimer peterg at rnaworld.bio.ukans.edu
Wed Jul 20 18:22:06 EST 1994


In <ehom1-190794135313 at image-slave.swarthmore.edu>, ehom1 at cc.swarthmore.edu (Erik Forbes Y. Hom) writes:
>Has anyone come across programs (that are freely available) that search out
>inverted sequences of RNA?  Actually, I'm interested in determining whether
>or not a mRNA sequence I have has regions through which it folds in such a
>manner as to delay its translation.  If you have some good suggestions on
>this subject, could you please post them on this bulletin board?  . . . . . . .

There are many programs which attempt to predict RNA secondary structure. None of then can 
actually do it perfectly, so beware. The output from these programs MUST be called a "predicted
(or possible) secondary structure'. I have used several, but I am not sure I'll be able to give
you the actual ftp/gopher sites. One nice commercial program for the PC is RNAFOLD (Scientific 
& Educational Software, (717) 597-5307). Free-ware would start with PC-FOLD (the Zucker 
program), available as pcfold (PC) or mulfold (MAC) from ftp.bio.indiana.edu (by Gopher). Other
programs should be in an RNA-specific gopher menu at merlot.welch.jhu.edu. There are also a 
number of powerful routines running under UNIX and VMS. These include programs by Zucker et al;
Martinez (UCSF); and Nussinov (I think). The commercial gene analysis packages all have some 
kind of RNA folding module. The Wisconsin CGC package is one; most of the PC and MAC packages 
do too -- DNASIS, PC-Gene, etc. 

Sorry I don't have addresses, etc., for these. I will make an effort to round up a complete 
listing and put it, along with PC and MAC software, on the rnaworld gopher server.

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