[ensembl-dev] How is Identity calculated?

[Sam Seaver]

In a list of orthologs computed by EnsemblCompara, Ensembl computes both
the Target %id and Query %id.

I suspect very much that this is the case of the number of identities being
divided by the length of the target or query sequence, but I'm curious as
to whether this includes the gaps that arise from the MSA?

Thanks
Sam

-- 
Postdoctoral Fellow
Mathematics and Computer Science Division
Argonne National Laboratory
9700 S. Cass Avenue
Argonne, IL 60439

http://www.linkedin.com/pub/sam-seaver/0/412/168
samseaver at gmail.com
(773) 796-7144

"We shall not cease from exploration
And the end of all our exploring
Will be to arrive where we started
And know the place for the first time."
   --T. S. Eliot
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