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

Jason Stajich jason at bioperl.org
Fri Jun 30 10:05:01 EDT 2006

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  


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

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