gcg codonpreference with 300,000 bases - problem

Jasper Rees - tel +44 865 275567 jasper at molbiol.ox.ac.uk
Tue Aug 3 05:37:04 EST 1993

In article <23j5loINNl2v at s-crim1.dl.ac.uk>, mbfw at s-crim1.dl.ac.uk (Frank Wright) writes:
> I have been looking at Yeast chromosome III (just over 300k long)
> using codonpreference with the -nopref and -bias=gc options, with
> the SGI and SUN Unix versions of GCG.
> The program hangs after drawing part of the first of the 3 frames
> - it doesn't draw the curve but just the tickmarks at the bottom
> of the first frame.  Although this sequence is less than 350K (the
> default sequence length maximum) maybe this problem has something to
> do with the length of the input sequence?

Mmmm, you don't say what you are setting for your X display options and I
don't know what these are for the unix versions... but for VMS the Black and
White X display has a bug which gives this effect in displays with large
amounts of this style of graphical output (there is an arrary that is too
small somewhere). I understand it has been tracked down and fixed. It could
well be in the same code that you are having problems with. 

It doesn't happen with greyscale or color X, or any of the other displays that 
I have used in the package, so this may give you a work around.

> Any ideas?  

Check out with GCG directly for a patch? Wait for version 7.3? 

> Frank Wright
> SASS, University of Edinburgh,
> Edinburgh, Scotland, U.K.
> frank @ sass.sari.ac.uk

Jasper Rees
Oxford University Molecular Biology Data Centre
and The Sir William Dunn School of Pathology

jasper at molbiol.ox.ac.uk

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