how to make a graphic secondary structure with letters ?

Don Gilbert gilbertd at sunflower.bio.indiana.edu
Tue Aug 31 19:42:40 EST 1993


My macintosh programs LoopViewer and LoopDloop provide essentially the
equivalent of GCG squiggles and much more, for free.  These programs will
read the same FOLD output files (the GCG .connect files) as squiggles,
and in one form will use essentially the same drawing algorithm as SQUIGGLES,
but you also have the option of better drawing algorithms.  The default is
to include letters of bases.  The LoopDloop version is a loop drawing Editor,
meaning you can rearrange the loops using macdraw-like methods.  Drawings from
LoopDloop have appeared in Science and other quality science publications (and 
my thanks to those authors who reference its use).

These programs are available by Gopher or ftp to ftp.bio.indiana.edu, in folder
molbio/mac/ as loopviewer.hqx and loopdloop.hqx

>> Hi GCG users,
>> I'm using FOLD to predict RNA secondary structures and SQUIGGLES to plot the r
>e
>> sults.. The output look very nice, but the secondary structures are curves wit
>h
>> out the corresponding base's letters
>> Since I need (for a paper) to show secondary structures with letters instead o
>f
>>  curves, I'm wondering if it is possible to obtain a similar output using GCG.
>> I can't use the no-graphic output of FOLD because it is not good enough ...
-- 
--d.gilbert--biocomputing office--indiana u--bloomington--gilbertd at bio.indiana.edu--




More information about the Bio-soft mailing list