BLAST: Trying to find parameters to get the same results via Python as via the NCBI BLAST web tool
Entering edit mode
7.6 years ago
tanny ▴ 10

I am running a nucleotide BLAST using Python/Biopython. However, I get less (67 hits) results than using the web BLAST (8660 hits) Biopython states that there are differences but does not point out how to adjust one's parameters to match those on the web interface.

Here is my code: from Bio.Blast import NCBIWWW result_handle = NCBIWWW.qblast("blastn", "nt", "GGCTGTATTCCCCTCCATCG", expect=10, hitlist_size=10000, megablast=False)

hitlist_size=10000 somehow does not return all hits but only hits that have a query cover of 100%. How can I get the other hits that have a query cover of less than 100%?

I experimented with various parameters but they only way to increase the number of hits was via "expect", the expected threshold, which is not exactly what I want.

Thanks for your help!

python blast ncbi biopython • 2.2k views
Entering edit mode

i'm upvoting this because your code is the only example of qblast parameters i could find in half a dozen searches - qblast is not well documented :/


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