[Biopython] (no subject)

[Matthias Schade]

Hello everyone,


I would like to run a blastn-query of a small nucleotide-sequence against a genome. The code works already, but my queries are still slow and mostly ineffective, so I would like to ask:

Is there a way to tell the blastn-algorithm that once a 'perfect match' has been found it can stop and send back the results?

Background: I am interested in only the first full match because I would like to design a nucleotide-probe which -if possible- has no(!) known match in a host-genome, neither in RNA nor DNA. Actually, I would reject all perfect-matches and all single-mismatches but allow every sequence with two or more mismatches.

Currrently, I use this line of code with seq_now being about 15-30 nt long:
result_handle = NCBIWWW.qblast("blastn", "nt", seq_now, entrez_query="Canis familiaris[orgn]")


I am still new to this. Thank you for your help and input,

Matt