[EMBOSS] Oddcomp behaves oddly ...

David Martin david at compbio.dundee.ac.uk
Wed Mar 8 10:26:23 UTC 2006

On 8/3/06 9:00 am, "Marc Logghe" <Marc.Logghe at devgen.com> wrote:

> ... Or rather, how should I use it properly ?
> OK, suppose your run compseq to obtain the frequency for individual
> residues:
> compseq tsw:Q62671 -word 1
> Apparently this example protein sequence is rather rich in leucine (106
> L out of 889).
> In order to detect this leucine bias, a little file was created
> (leu.comp) that had the following content:
> <file leu.comp>
> Word size       1
> Total count     0
> # bias should be detected as 106 > 100
> L       100
> </file leu.comp>
> Oddcomp was run like this:
> oddcomp tsw:Q62671 -infile leu.comp -window 889

Try window 888 (ie shorter than the length of the sequence). There are a
couple of minor bugs in the oddcomp code that I will forward to the team.

Basically what is happening is that there is a check for the length of the
sequence being shorter than the window.  It may well be this that is giving
the problem. 

It is a long time since I wrote this and C is not my usual language so
apologies if this is not a comprehensive answer.


> But the sequece is not reported.
> When I change the L count to 10 in leu.comp it does not work neither.
> Strangely enough, when the default window is taken (30) the sequence is
> reported.
> What is happening here ?
> Regards,
> Marc
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