[Bioperl-l] simpleAlign percentage_identity

[Heikki Lehvaslaiho]

Jason Stajich wrote:
> 
> I think that percentage identity was not being calculated correctly in
> SimpleAlign.
> 
> It seems the calculation of the divisor is wrong - or we need to stop
> double counting the total identical.  I have committed a fix that seems in
> line with what EMBOSS is reporting for overall percent identity (strangely
> emboss water 2.2.1 and emboss water < 2.2.1 do not agree on percent
> identity for the same data...).  All tests pass so I'm committing the
> change.  Please have a look.  It is a simpler solution I believe since we

Seems to be fine now.

	-heikki

> can rely on the length of alignment to tell us how many possible sites to
> compare (if we're including gaps in the percent id calculation).
> 
> I have also committed changes which should handle both the needle output
> where it doesn't include leading/trailing gaps for global alignments and a
> more correct percentage_identity calculation in SimpleAlign.
> 
> Marching on...
> 
> -j
> --
> Jason Stajich
> Duke University
> jason@cgt.mc.duke.edu
> 
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-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
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