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

Sendu Bala bix at sendu.me.uk
Wed Aug 2 07:23:01 EDT 2006

Andreo Beck wrote:
> Can $hit_object->frac_aligned_hit or $hit_object->frac_aligned_query
> give outputs > 1 ? I get some > 1 values.

This should now be fixed in CVS. You should be able to grab just 
Bio/Search/SearchUtils.pm if you don't want to install all of bioperl-live.

( http://code.open-bio.org/cgi/viewcvs.cgi/bioperl-live/ )

It should be noted that all frac_* statistics and probably others from 
hit objects have had a high chance of being wrong in the past, and 
frac_identical and frac_conserved can still be very wrong*. It would be 
a good idea if someone were to make these methods return slightly more 
sane numbers.

[*] which is to say, more wrong than you might reasonably expect, given 
the limitations with gapped or alignment-free blasts

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