(biopython) qblast taking half hour - one search?
(Newbie)
I am trying to get alignments of one organisms proteins from mass-spec against another organisms. As input I have a file with all the protein sequences I want to query a database with. For example "bovine_ms_aa["Bovine_Seq"][0]" is of the from 'MEAK...DE'.
Following the Biopython Tutorial/Cookbook, I have this running in my jupyter-notebook.
NCBIWWW.qblast("blastp", "nr",bovine_ms_aa["Bovine_Seq"][0])
But it has not yielded any results for over 30 minutes. When I try on the NCBI website, I get a final results in <60s.
Might there be something wrong with the syntax? I have looked it over and don't see the error.
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jacob_r_anderson •
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Try this example command given by the book
It gave me the result within three minutes.
How many peptides are in your dataset?
Have you tried running BLAST locally?