The ncbi online blast tool has an option of limiting the 'max matches in a query range' so that one section of your sequence doesn't fully consume all of the blast hits, leaving other portions of the segment uncharacterized by the blast. However, I can't seem to figure out a way to be NCBIWWW.qblast to have a similar result.
The only work-around I have found is to ramp up the hitlist_size (to 10,000) & filter through the blast results based on where they hit my query. While doable, I would feel more confident in the results if I could limit the 'max matches in a query range' while also keeping the file sizes down.
Anyone know of an option in NCBIWWW.qblast that allows this?
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I don't know NCBIWWW.qblast but I am assuming it runs NCBI BLAST+. In this case, I think what you're looking for is the BLAST+ -culling_limit option.
NCBIWWW.qblast is a biopython module that allows you to BLAST over the web (which I am hoping to do since I am using the BLAST DB refseq_protein). But it's looking like I may need to sacrifice speed for confidence in results & use BLAST+ w/ culling_limit. Thanks for your suggestion!
http://biopython.org/DIST/docs/api/Bio.Blast.NCBIWWW-module.html