I am trying to find a DNA sequence homologous to a given coding sequence in a specific organism (E. fergusoni, to root an E. coli genes phylogeny)
I want to blast one of my focal species’ sequence and get back all sequence from E. fergusoni that have between 80% and 98% similarity on the whole segment.
This work prety well on the NCBI online version of blast, by setting “Escherichia fergusonii (taxid:564)” in the “Organism” field. However, I want to automatise this process to be able to run it quickly on a large set of disinct E. coli genes.

I want to use the NCBIWWW.qblast function from the Blast module with argument “entrez_query” to specify the organism I want to restrain my research to.

This is what I tried :

Blast.email = [email protected]
from Bio.Blast import NCBIWWW
from Bio.Blast import NCBIXML

sequence_data = open("gene0.fasta").read()
result_handle = NCBIWWW.qblast(
    program="blastn",
    database="nt",
    sequence=sequence_data,
    # entrez_query = "txid564[Organism]",
    # entrez_query = "Escherichia fergusonii (taxid:564)[Organism]",
    # entrez_query = "txid564[ORGN]",
    # entrez_query = "564[Taxid]",
    format_type="XML",
)

with open("gene0_results.xml", "w") as out_handle:
    out_handle.write(result_handle.read())



for record in NCBIXML.parse(open("gene0_results.xml")): 
    if record.alignments: 
        print("n") 
        print("query: %s" % record.query[:100]) 
        for align in record.alignments: 
            for hsp in align.hsps: 
                if (hsp.identities/len(hsp.query) < 0.98) and (hsp.identities/len(hsp.query) >= 0.8)  : 
                    print("match: %s " % align.title[:100])
                    print(f"length: {align.length}")
                    print(f"e value: {hsp.expect}")
                    print(f"identity : {hsp.identities/len(hsp.query)} ({hsp.identities} nucleotides over {len(hsp.query)})")
                    print(hsp.query[0:75] + "...")
                    print(hsp.match[0:75] + "...")
                    print(hsp.sbjct[0:75] + "...")

When I run this script without uncommenting the entrez_query arguments, I get the E. coli sequences that are 100% similar to my query, in about 1 mn.
But when I uncomment one of them, I don’t get any result at all (I also checked the XML file to see if my later filtering was not the reason), and the request can take up to 20mn. I am looking for the correct syntax to specify the organism with entrez_query (I tried different ones based on what I saw on other posts or what seemed intuitive) but none of them give any result, contrarily to the internet blast version.

I am using Python 3.11 and Biopython 1.83 in a Jupyter Notebook with VSC 1.89.1