I'm trying to use Biopython to do a psi-blast search via the internet for homologous proteins. Unfortunately I'm having several problems with this that I could use some help with.
The returned XML files seem to be abruptly truncated. When Biopython attempts to parse these files it gets XML reading errors. When I examine these files by hand I see that most of the files do not have all the XML tags closed. Most files end at a </hsp> tag without closing off the iteration tags. 2.
I can't find an argument to specify the # of iterations psi-blast should perform in the Biopython qblast function.
I'd appreciate any help. I imagine my description might be too vague. If so, I'd be happy to post a more detailed description once i get out of the microscope room.
I'm using version 1.62 on the newest OSX.