I’m trying to blastp multiple aminoacids sequences using biopython. I just can’t seem to get it right and i cant figure out the handbook for how to do this. I have come up with the following:
open("proteins_PROT.fasta","r")
from Bio.Blast.Applications import NcbiblastpCommandline
cline = NcbiblastpCommandline(query="proteins_PROT.fasta", db="nr",
evalue=0.001, remote=True, ungapped=True)
NcbiblastpCommandline(cmd='blastp', query="proteins_PROT.fasta", db='nr', evalue=0.001,
remote=True, ungapped=True)
print(cline)
blastp -query proteins_PROT.fasta -db nr -evalue 0.001 -remote -ungapped
How do i run a blastp result with multiple sequences in a fasta?
Thank you
Read more here: Source link