[Bioperl-l] $hit_object->frac_aligned_hit/$hit_object->frac_aligned_query

Sendu Bala bix at sendu.me.uk
Wed Aug 9 04:43:58 EDT 2006

Bernd Brandt wrote:
> Hi,
> "frac_identical and frac_conserved can still be very wrong"
> They were wrong with hmm report parsing (hmmsearch). The  bioperl-live
> (CVS 14 July 2006) returned 0 for both fracions. I will check it with
> the newest CVS and send a small test script.

For both hmmsearch and hmmpfam parsing, those are deliberately set to 0. 
They needn't be; there is a midline to the hsp-like-thing that shows 
identical and conserved positions. I suppose the reason they're set to 0 
currently is that its not a real alignment against a set sequence, but 
against a model. Still, I think it's reasonable to give an answer in 
both cases if you can get an answer from the original output files.

I'm in the process of writing new hmmer parsers, and will allow non-0 
answers for those methods.

(Its not really possible to alter the existing parser because it only 
allows one hsp per hit, preventing a correct answer even if it didn't 
set to 0)

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