how to make a graphic secondary structure with letters ?

Peter Rice rice at embl-heidelberg.de
Mon Aug 30 07:08:39 EST 1993

In article <1993Aug27.142322.3855 at gserv1.dl.ac.uk>,
DELLE%IPCUCSC.earn at uk.ac.earn-relay (Massimo Delledonne) writes:
> Hi GCG users,
> I'm using FOLD to predict RNA secondary structures and SQUIGGLES to plot the re
> sults.. The output look very nice, but the secondary structures are curves with
> out the corresponding base's letters
> Since I need (for a paper) to show secondary structures with letters instead of
>  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 ...
> (And my sequence is long a lot ...)
> Any suggestion ?

No problem. As usual with GCG, try the "optional parameters" first (look in
the program manual under "optional parameters" at the end of the documentation
for the program you are using, look in GenHelp progname option, or just run
the program with /check to show the command line options).

In this case, SQUIGGLES /SHOWSEQ will put the sequence on the plot. You can
also just show part of the sequence (main stem-loop for example), adjust or
remove the numbering, set the height of the sequence characters, and pivot
parts of the structure to make the plot look better (or to make room for the
sequence characters).

You also have all the standard GCG graphics options to change color, scale,
font, orientation, and so on when preparing graphics for publication.

 Peter Rice, EMBL                             | Post: Computer Group
                                              |       European Molecular
 Internet:    Peter.Rice at EMBL-Heidelberg.DE   |            Biology Laboratory
                                              |       Postfach 10-2209
 Phone:   +49-6221-387247                     |       69012 Heidelberg
 Fax:     +49-6221-387306                     |       Germany

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