How To Show More Blast Results Using Biopython?

Question

[Niek De Klein]

Hi,

I'm using biopython to BLAST over the internet. However, it only saves 30 results (there are more than 30 results that are under the e-value I chose) in the xml. I've been looking all over but can't find how to make that number higher. So my question is, how can you show more results from BLAST using biopython. I'm using NCBIWWW.qblast from BIO.BLAST.

from Bio.Blast import  NCBIWWW
File = "MIF"
fasta_string = open(File+".fasta").read()
result_handle = NCBIWWW.qblast("blastp", "nr", fasta_string)

Thanks, Niek

[User 59]

Which blast service are you using?

[Niek De Klein]

NCBIWWW.qblast

File = "MIF"
fasta_string = open(File+".fasta").read()
result_handle = NCBIWWW.qblast("blastp", "nr", fasta_string)

[Niek De Klein]

I editted it in my post.

Answer 1

[Science_Robot]

From here:

qblast(program, database, sequence, 
       ncbi_gi=None, descriptions=None,
       alignments=None, expect=None,
       matrix=None, filter=None,
       format_type=None, hitlist_size=None,
       entrez_query='(none)')

Did you try setting descriptions, alignments, and/or hitlist_size?

[Niek De Klein]

Yes thank you! I've been looking for a site like that.

Answer 2

[User 59]

According to this post here (a little outdated I admit), you will want to override the hitlist_size defaults.

Answer 3

[Peter]

Hello Niek,

Daniel pointed out an email to the Biopython mailing list which answers your question - basically try reading the built in documentation. This is also mentioned in the Biopython Tutorial, quote:

For more about the optional BLAST arguments, we refer you to the NCBI’s own documentation, or that built into Biopython:
from Bio.Blast import NCBIWWW
help(NCBIWWW.qblast)

Also audyyy pointed out some old (but apparently still relevant) documentation from Andrew Dalke's homepage.

You said

I've been looking all over but can't find how to make that number higher.

so you probably looked at some of these bits of documentation (right?). Could you suggest how it could be made clearer for newcomers? Feedback does help to improve the docs.

Thanks,
Peter