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Bruno Kieffer's GCG secondary alignment question.

Steve Thompson: VADMS genetics THOMPSON at JAGUAR.CSC.WSU.EDU
Wed Jan 12 12:43:45 EST 1994

Hello all -

In Message-Id: <9401120921.AA19753 at net.bio.net> Bruno Kieffer 
(kieffer at bali.u-strasbg.fr)


>	Does anybody knows a program able to read a multi-alignment
>file (msf) from the UWGC command PILEUP, and align secondary structure
>predictions obtained for each sequence ?

I just finished doing one for a client here working with Q fever.  I strictly
used GCG routines --- takes a bit of trickery and a working knowledge of their
Figure language.  The results are well worth it though --- publication quality
PostScript.  Requirements are GCG, a terminal capable of displaying GCG
graphics as well as editing, a Postscript printer, and lots of patience.

Start with your "best" msf file and change all of the gaps "." to unknowns "x"
using whatever editor you like.  This is necessary because none of the
structural analyses programs will accept the gap caharacter.  Rationally it
shouldn't make any difference since the structural informational content of
both a gap and an unknown is nothing.  Unless you use a sequence editor of some
sort that recalculates checksums as it closes, YOU MUST REFORMAT YOUR MSF FILE. 
Thus on VMS:

		$ Reform/MSF your_best.msf{*}

Notice the "{*}" --- this is very important in GCGese; it means "all of the
sequences in the msf file.  Next, Run PepPlot analyses on each INDIVIDUAL
sequence from the msf file.  Specify which panels you want to display (the
fewer the better; we just did hydropathy).  A command line to hydrophaphy scan
for transmembrane spanning helices in an opsin may be:

$ PepPlot/Menu=J/HWind=21/GESWind=21/In=opsin.msf{oohug}/Figure=oohug.plot

Pick one of the produced Figure plots to serve as the framework for the final
graphic and load it into your favorite editor.  Now dive into the GCG Figure
program and delete command lines in the file as you desire.  For instance, the
..pt PEPPLOT OF ... line draws (plots text) the header at the top of the
graphic and should probably be deleted or changed to an appropriate title. 
Another example of a change that can be made is editing out entire line traces;
e.g. the above command line produces a plot with both a black KD and a green
GES plot trace.  Find the point in the file where .nc 2 occurs (new color
green) and delete all of the following draw (.d) commands until the next
section.  Go wild and modify the file any way you like, EXCEPT remember what
you do because you need to make exactly the same changes in EACH of the plots
that you wish to align.  Modify all of the Figure files the same way (except
the title of course should only be on the top most plot).  Check your work by
displaying the Figure files to your terminal with the Figure command.
Finally at the very bottom of the framework (top most) plot file (because
that's the way I think) insert the include command providing exactly the same X
coordinate viewport locations as the original but appropriate Y coordinates to
locate it just below the original.  This will take some interactive playing
around with to get right, but you can stack as many of them on top of another
as you want.  For example, at the bottom of a "framework" figure file ...

	.pt Kyte-Doolittle
	.nc 1
	.m 89.8 67.2
	 blah blah blah blah blah blah .......
	.include oohug.plot 0 150 -20 80
	.include oohur.plot 0 150 -50 50
	.! End Page 1

would produce a plot of three aligned opsin hydropathy plots, the framework one
over green over red.  Once the graphic appears on your screen just the way you
want it (use the various options of Figure to get it EXACTLY right on the
screen. e.g. /xscale /yscale /xpan /ypan), reinitialize to EPSF format and
duplicate the Figure run.  This will produce the same image as you had on the
screen only as an Encapsulated PostScript File with maximum resolution
possible.  The results are publication quality.

Hope this helps; sorry for the length --- I tend to do that.  Now if some
bright person could just write a fancy script to do all that I described ....

							- Steve

                              Steven M. Thompson
            Consultant in Molecular Genetics and Sequence Analysis
VADMS (Visualization, Analysis & Design in the Molecular Sciences) Laboratory
           Washington State University, Pullman, WA 99164-1224, USA
          AT&Tnet:  (509) 335-0533 or 335-3179  FAX:  (509) 335-0540
                  BITnet:  THOMPSON at WSUVMS1 or STEVET at WSUVM1
                   INTERnet:  THOMPSON at wsuvms1.csc.wsu.edu

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