Running BLAST from Python

# Import the modules for interfacing with BLAST and parsing the output

from Bio.Blast import NCBIWWW, NCBIXML

# Blast the sequence of interest (in this case using the accession number

result_handle = NCBIWWW.qblast("blastn", "nr", "8332116")

# Parse the resulting output

blast_record = NCBIXML.read(result_handle)

# Loop over the alignments printing some output of interest

E_VALUE_THRESH = 0.004

for alignment in blast_record.alignments:

for hsp in alignment.hsps:

if hsp.expect < E_VALUE_THRESH:

print '****Alignment****'

print 'sequence:', alignment.title

print 'length:', alignment.length

print 'e value:', hsp.expect

print hsp.query[0:75] + '...'

print hsp.match[0:75] + '...'

print hsp.sbjct[0:75] + '...'

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