[EMBOSS] Oddcomp behaves oddly ...

Marc Logghe Marc.Logghe at DEVGEN.com
Wed Mar 8 09:00:14 UTC 2006

... Or rather, how should I use it properly ?

OK, suppose your run compseq to obtain the frequency for individual
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

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
What is happening here ?


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