[Bioperl-l] Bio::SearchIO::hmmer hsp behaviour

Chris Fields cjfields at uiuc.edu
Fri Jun 30 11:56:09 EDT 2006

It may have been just simpler to have it be one HSP (domain) per Hit  
(model) as that's how the reports are generated.  My reasoning was  
that using the one domain per model made sense based on what you are  
actually trying to do, which is annotate the sequence based on the  
order the domain appears.  Most others may not view it that way,  
which is fine.  One can always gather the relevant HSP's, convert to  
seqfeatures, then sort them if order is important, I suppose.

I would say, if the overall consensus is to modify it to have  
multiple domain hits per model (similar to BLAST) then Sendu should  
go ahead and make those changes then announce it on the list so no  
one can gripe about it later.  My main concern was not changing  
things so dramatically that it'll break for someone, but seeing as  
we've had a lengthy discussion about it already they should have  
piped up by now!   Well, that and trying to return everything as  
hashes as Jason suggested.  From looking at SearchIO::hmmer we need  
to make sure that both hmmsearch and hmmpfam work the same way (looks  
like they have different sections) and that the reported bug about  
missing hits (Bug 2036) is fixed as well.


On Jun 30, 2006, at 9:05 AM, Jason Stajich wrote:

> I understand the confusion and it was the intention of having HSPs
> grouped together under the same Hit initialy just like BLAST reports
> - but somehow in the bug-fix-cycle the way to deal with the fact that
> "HSPs" aren't ordered by the overall Hit table led to this design
> decision - the problem before was something with the ordering, but I
> must admit to not being able to remember what specifically was the
> problem t I can't really remember why I changed things to do this.
> Does 1.4 actually do it the way you expect?
> Again, more user feedback is definitely critical to make these tools
> useful to everyone so please don't bashful about reporting your
> preferences.
> -j
> On Jun 30, 2006, at 8:45 AM, Bernd Web wrote:
>> Hi,
>>> My original question was essentially: does doing it my way make
>>> sense?
>> With respect to Sendu's points, I can only say that a colleague
>> (developer) and I were surprised that the HMMer parser did not group
>> the hits as the blast parser does, in "Hit" and "Hsp".
>> When we realized how hmmer parsing worked we continued with to use it
>> but used a check for multiple hits of one domain on 1 query sequence
>> (e.g. in hmmpfam).
>> Regards,
>> Bernd
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> --
> Jason Stajich
> Duke University
> http://www.duke.edu/~jes12
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign

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