(biopython) qblast taking half hour - one search?

Question

[jacob_r_anderson]

(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.

[Sishuo Wang]

Try this example command given by the book

result_handle = NCBIWWW.qblast("blastn", "nt", "8332116")

It gave me the result within three minutes.

[Joe]

How many peptides are in your dataset?

Have you tried running BLAST locally?