[BioPython] blast

[Stefanie Lück]

Sorry, I forgot to say that I do the alignment myself. It's was just for 
demonstration.

Yes. I have a 30 bp primer. 15 bp from the primer bind to my query sequence. 
The percentage would be 50 %.
percent = match * 100 / full length primer

>
percentage_identity = (100.0 * hsp.identities) / hsp.align_length
percentage_identity_ref_matched_query = (100.0 * hsp.identities) / 
(hsp.align_length - hsp.query.count("-"))
>

Sorry, both give me wrong percentage if I try on my database.

Look here, compare alignment and percentage:

http://picasaweb.google.de/luecks/Python02/photo#5226228430697476754

e.g Hit 13 should give 60 %

What you recommend to use instead of hsp.score?

Nice quitting time
Stefanie