[BioPython] blast

[Peter Cock]

> Thanks, I got another formula which seems to work well too (and which
> seems cleaner than counting the number of '|') :
>
> float(100) * float(hsp.score) / float(alignment.length)

I don't think that gives you the same thing as the percentage identify
(see my other email).

>> Have you considered actually showing the blast alignment too?
>>
> Yes, it's in the output, I just replaced the '|' with a red background
> and the ' ' with a green background, so they see directly where it
> doesn't match

Since the graphical representation of the match/mismatch string is
done using the colours red and green, it is useless for anyone who is
colour blind.

Also the user can't cut and paste the alignment into an email or other
document (electronic lab book?), which seems like an obvious thing to
want to do.

Personally, I would try and keep the output looking more similar to
traditional blast, as then its easier to understand (assuming you
already know BLAST!).

Peter