Question: (Closed) blast against genomes in biopython
5.4 years ago by
halima.loulou • 0
halima.loulou • 0 wrote:
from Bio import Entrez, SeqIO from Bio.Blast import NCBIXML from Bio.Blast import NCBIWWW result_handle = NCBIWWW.qblast("blastn","nr", "CACTTATTTAGTTAGCTTGCAACCCTGGATTTTTGTTTACTGGAGAGGCC",entrez_query='"Beutenbergia cavernae DSM 12333" [Organism]') blast_records = NCBIXML.parse(result_handle) for blast_record in blast_records: for alignment in blast_record.alignments: for hsp in alignment.hsps: print(hsp.query[0:75] + '...') print(hsp.match[0:75] + '...') print(hsp.sbjct[0:75] + '...')
this does not give me an output, although the sequence is actually a sequence of the genome, so i must get a result. where is the error? the query is correct?
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