[Bioperl-l] Bio::SimpleAlign - Meaning of overall_percentage_identity?

[Dave Messina]

Hi Giuseppe,

If I understand correctly, the method works by considering only aminoacids
> that are identical over all the members of the alignment


Yes.


> , and then averaging over the total number of aminoacids in the sequence.
> Is this correct?
>

Almost.

By default, the denominator is the alignment length, namely the length of
the MSA including gaps. By means of the 'short' and 'long' options, it's
also possible to use the shortest or longest sequence's ungapped lengths as
the denominator.


Dave