[Biopython] NCBIWWW.qblast Expect value / E-value
Jasper Koehorst
jasperkoehorst at gmail.com
Wed May 20 12:51:13 UTC 2009
Im running against problems when i try to identify short peptide sequences
of ±10 - 20 peptides. When i run this at the NCBI Blast website i get
results, these all have
high E-Values that i dont really care at the moment. The problem is when i
do this in biopython as stated below, i will not get any results...
I believe this is due to the fact that biopython will not show results with
a "high" E-Value. Is there a way to change this? So it will allow results
with an E-value of ±1500
or more?
I tried the sript below but that does not quit work...
Anybody has an idea?
result_handle =
NCBIWWW.qblast("blastp","nr",peptide[1],entrez_query=i, expect=2000,
matrix_name='BLOSUM80')
blast_records = NCBIXML.parse(result_handle)
blast_record = blast_records.next()
E_VALUE_TRESH = 10000000
for alignment in blast_record.alignments:
for hsp in alignment.hsps:
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