[EMBOSS] Oddcomp behaves oddly ...
Marc.Logghe at DEVGEN.com
Wed Mar 8 11:36:06 UTC 2006
I am afraid there are some remaining oddities with oddcomp.
Tried another protein, other residue.
Word size 1
Total count 0
First a set of sequences is generated (kind of mimicking sliding window)
of length 20:
splitter wormpep:ZK822.4 -size 20 -overlap 19 > split.fa
Second, oddseq is run (with window option off by one):
oddcomp split.fa -window 19 -infile compseq.data
# Output from 'oddcomp'
# The Expected frequencies are taken from the file: compseq.data
# Word size: 1
# END #
The first 20mer:
It is clear that there are 7 S residues in this stretch and we were
looking for 4 or more, so that makes sense.
However, when you run oddseq again with S count of 5 instead of 4, no
sequence is reported !
> -----Original Message-----
> From: David Martin [mailto:david at compbio.dundee.ac.uk]
> Sent: Wednesday, March 08, 2006 11:26 AM
> To: Marc Logghe; emboss at emboss.open-bio.org
> Subject: Re: [EMBOSS] Oddcomp behaves oddly ...
> 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
> > is reported.
> > What is happening here ?
> > Regards,
> > Marc
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