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Blast in Biopython

hello, I have two sequences and i need to use Blast under Biopython to align these two sequences and retrieve the results in list for example. But i can't do this. can you explain me using commande line please? thanks

blast alignment biopython
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written by midox midox

Can you show us what you tried and what didn't work? People will be more eager to help you when you show some effort from your side.

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written by WouterDeCoster WouterDeCoster

here is a simple description of my program:

from Bio import SeqIO
import os
import sys
from Bio.Blast.Applications import NcbiblastnCommandline

com = NcbiblastnCommandline(query = "GGCTAGCTTT", subject = "GGCTTTCTTT", out = 'blast2')
myStdout, myStderr = com()

but here the problem is query and subject must a files. can i use directly a sequences? Thanks

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written by midox midox

You posted earlier with an indication that you had already done this: calculate the e-value of alignment Since your question about e-values has not bee answered are you retrying to get an answer with this new question?

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written by GenoMax GenoMax

no it's not the same problem. the e-value problem is : i have created the SW matrix and i would determinate the e-value according to the values used in BLAST but the problem is my sequences is very long so the creation of SW matrix and recuperate the results is too long. Here, i try another solution using BLAST directly in Biopython, i would do an alignment between two sequences using BLAST under Biopython(standalone or in internet). if it's rapid so used this method but I do not know how to use BLAST under python. I try to use it.

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written by midox midox

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