[ensembl-dev] How is Identity calculated?

Matthieu Muffato muffato at ebi.ac.uk
Fri Nov 28 11:17:19 GMT 2014

Dear Sam,

%id is the number of identical matches divided by the length of the 
considered sequence. Gaps (bits of that sequence that are not matched on 
the other sequence) are thus included


On 26/11/14 19:03, Sam Seaver wrote:
> 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

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