[EMBOSS] Oddcomp behaves oddly ...

[David Martin]

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.

..d

> 
> 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
> 
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at emboss.open-bio.org
> http://newportal.open-bio.org/mailman/listinfo/emboss