[Bioperl-l] Bio::Tools::BPlite::HSP - percentage IDs

[Jason Stajich]

Hmm, I really hadn't ever looked at that code - What are the arguments for
or against.  

We can have a flag be twiddled to determine whether or not to use
subject or query, but are both technically correct? 

-Jason

On Wed, 11 Jul 2001, simon potter wrote:

> Hello.
> 
> I've a question about parsing Blast output and how to get percentage
> sequence identity.
> 
> In HSP.pm it is calculated by dividing the number of matches by the query
> seq length, rather than the subject seq length (i.e. a re-calculation of
> the % given in the blast output).
> 
> Is there a reason for calculating it in this way? I've talked to people
> around here and the general feeling is that it's better to calculate wrt
> the subject seq.
> 
> Question is - what to do about this? Is this something we should change -
> maybe a solution is to provide a choice for how we %id?  What do people
> think?
> 
> Thanks,
> 
> Simon Potter,
> EnsEMBL team, Sanger
> 
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Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/