[Biopython] To do Blast alignment of two proteins by biopython

[Benjamin Li]

Hi all,

I have posted the same question on BioStar, but I think some of the
Biopython users may not check Biostar so I also post it to the mail list.

I am new to biopython and I am not sure if it is a stupid question.

I would like to perform the same task as the one can be done on the web
based blast.

I am trying to align two protein by providing their GIs and receive the
e-value. But I can only find examples to blast one protein in the biopython
tutorial.

How can I align two protein using the qblast function?

I have tried the command

result_handle = NCBIWWW.qblast("blastp", "pat", "330186","118881")

But it returns me a lot of alignments and a lot of e-values.

I also found that it takes a few minutes for my computer to complete the
query, where if I use the web based blast only takes a few seconds.

Is my query anything wrong?


Merry Christmas!

Benjamin Li