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.
1.
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.
Thanks
•
written
by
eric.lubeck •
1 answer
Five years ago the NCBI said their QBLAST web-API does not support PSI-BLAST, so you would be better off using the standalone BLAST+ binaries at the command line (optionally via the Biopython wrappers). See:
- http://lists.open-bio.org/pipermail/biopython/2008-May/004231.html
- ...
- http://lists.open-bio.org/pipermail/biopython/2008-May/004234.html
- http://bugzilla.open-bio.org/show_bug.cgi?id=2496
- https://redmine.open-bio.org/issues/2496
Someone asked something similar on Reddit recently http://www.reddit.com/r/bioinformatics/comments/1qmpbm/problems_with_psiblast_results_from_biopython/ which was flagged on the Biopython mailing list http://lists.open-bio.org/pipermail/biopython-dev/2013-November/010976.html
If you posted your code, it might help us modify Biopython to give a clearer error message?
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show the parts of the program that saves the XML files.
Are you using remote blast? I do get some similar problems when doing a remote blast, it seems to be solved when you make a local copy of the DB or blast against a local DB.