Question: Problems With The Xml Output Of Psi-Blast Via Qblast When Using Biopython
0
gravatar for eric.lubeck
5.4 years ago by
eric.lubeck0 wrote:

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

biopython • 1.6k views
ADD COMMENTlink modified 5.3 years ago by Peter5.8k • written 5.4 years ago by eric.lubeck0
1

show the parts of the program that saves the XML files.

ADD REPLYlink modified 5.4 years ago • written 5.4 years ago by Istvan Albert ♦♦ 79k

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.

ADD REPLYlink written 5.4 years ago by Venky20
0
gravatar for Peter
5.3 years ago by
Peter5.8k
Scotland, UK
Peter5.8k wrote:

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:

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?

ADD COMMENTlink written 5.3 years ago by Peter5.8k
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