[Bioperl-guts-l] [Bug 2203] Signalp extension or new module

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Wed Mar 21 07:31:25 EDT 2007


http://bugzilla.open-bio.org/show_bug.cgi?id=2203





------- Comment #13 from emmanuel.quevillon at versailles.inra.fr  2007-03-21 07:31 EST -------
(In reply to comment #12)
> Added Neil and Ronald's modified Signalp to CVS and modified Signalp.t to
> reflect that v3 now parses.  
> 
> Neil, I think the answer to your question is 'yes', in that we should plan on
> merging the functionality of the two modules in some way (if anyone has the
> time to take that on it would be great!).  Having two Signalp modules is a bit
> confusing but may have to do for the time being.
> 
> In the meantime we'll leave this open to keep track.
> 

Hi Chris, hi Neil,

Regarding the modification from Neil, it is a good thing. Nevertheless, if you
look closely the code for Signalp module, you'll see that it only returns
results for scores 'mean S' and 'max Y'. Moreover it is more stringent because
it needs to have 'YES' for this two scores to get a Seq feature.
On the other hand, my module is able to return all results, wihtout any filter
or and can filter on 0 to 5 score and returns only sequence having 'YES' for
these scores whereas the original Signalp only takes into account 'mean S' and
'max Y'.
So the question is, should we only keep this stringent filter from original
Signalp, or introduce more flexibility by using mine?

I'll try to add some more functionalities by being able to parse 'short'
output, where the results are displayed on one line. Do youthink this could be
a good improvement?

Regards

Emmanuel


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