Investigate the effects of using hsp.identities/float(record.query_length) >= tol vs max_identity >= tol

[mscook]

[happykhan]

I use the following in Dryad to allow users to specify a minimum % identity over a minimum % of gene length. (where lenCutOff is the percentage of original gene length that must be covered by the match & identCutoff is the percentage identity across the match itself)

if ( float(hsp.identities) / float(hsp.align_length) * float(100) ) > float(identCutoff)
and ( float(hsp.align_length) / float(alignment.length) * float(100) > lenCutoff):

[mscook]

Thanks Nabil. Discussed with Brian & Nouri today and am going to implement some additional scoring schemes. I like the one above.