Biopython's NCBIWWW.qblast tblastn problem
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5.5 years ago

I'm having trouble using qblast with tblastn. Certain assemblies will return the correct sequences below my specified e-value, but other assemblies will return nothing. When the same queries that show no results are done on NCBI's website, it shows that I should be getting sequences returned. I'm questioning whether it's because I'm using the GCA assembly number, or if I need to being using the GCF number. I'm not really sure what the differences are between the two assembly types. I've been using the GCA from: genomes . I have realized that not all genomes have both; GCA and GCF numbers.

CODE:

idnum are found from the source code, if you select genome database and enter a specific GCA. From there you click BLAST search this assembly view source code from there. The id number are listed near the bottom of the source.

     results = NCBIWWW.qblast("tblastn","genomic/"+idnum+"/"+gcanum, sequence=searchquery, format_type="XML")
biopython python qblast ncbiwww • 1.3k views
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