Re: Request: RNA folding prog. w/ ~2.5 kb RNA?

Article View: bionet.software

Article #2279

#2279

From: Don Gilbert
Date: Sat, 25 Jun 1994 14:26

20 lines
1735 bytes

modifying the source to mfold or other rna folding program is
your main option.  The reason large molecules like 2.5kb are not
normally supported is that it takes a huge chunk of memory
for a program to deal with rna folding that size, and a lot
of cpu time.  Be prepared for a good long wait, depending
on how fast your computer is, for the results.  I think analysis time
is proportional to the cube of the size of the molecule.

Your GCG version of mfold source is likely on your computer
in the gcg/source location.  But if you can't find it, you can
dig up Michael Zuker's original mfold source at this ftp location:

nrcbsa.bio.nrc.ca:
        -Michael Zukers software for folding with multiple suboptimal
         scores, viewing of structures and more.


-- Don
-- 
-- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu

Technical Details

Message-ID: <CryIrr.CCK@usenet.ucs.indiana.edu>

Path:

arc1-ca.pugleaf.net!bga.com!news.sprintlink.net!news.onramp.net!convex!cs.utexas.edu!usc!sol.ctr.columbia.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd

References: <CrvA4s.4vr@cgl.ucsf.edu>

Show Full Headers

Complete Article Headers

X-Google-Language: ENGLISH,ASCII-7-bit
X-Google-Thread: 103fe7,c0c030fe28d3368d
X-Google-Attributes: gid103fe7,public
X-Google-Thread: fa6b6,c0c030fe28d3368d
X-Google-Attributes: gidfa6b6,public
X-Google-ArrivalTime: 1994-06-25 10:27:34 PST
Newsgroups: bionet.software,bionet.software.gcg
Path: arc1-ca.pugleaf.net!bga.com!news.sprintlink.net!news.onramp.net!convex!cs.utexas.edu!usc!sol.ctr.columbia.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd
From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert)
Subject: Re: Request:  RNA folding prog. w/ ~2.5 kb RNA?
Message-ID: <CryIrr.CCK@usenet.ucs.indiana.edu>
Sender: news@usenet.ucs.indiana.edu (USENET News System)
Nntp-Posting-Host: sunflower.bio.indiana.edu
Organization: Biology, Indiana University - Bloomington
References: <CrvA4s.4vr@cgl.ucsf.edu>
Date: Sat, 25 Jun 1994 14:26:15 GMT
Lines: 20

Reply to Parent Message