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Compare 2 local protein FASTA using NCBI BLAST Biopython

I have 2 protein sequences I need to compare using NCBI BLAST

  1. the protein sequence as listed in a gbk file identified by the CDS

  2. the protein sequence that is translated from the nucleotide sequence denoted by the CDS location

    import sys
import os
from Bio import SeqIO
from Bio.SeqFeature import SeqFeature, FeatureLocation

for record in SeqIO.parse(fullpath, "genbank"):
    if record.features:
        for feature in record.features:
            if feature.type == "CDS":

                translated_protein = str(feature.qualifiers.get('translation', 'no_translation')).strip('\'[]')
                cds_to_protein = str(feature.extract(record).seq.translate(to_stop = True))

            if translated_protein != cds_to_protein:
            ##run blast on translated_protein and cds_to_protein

Is that possible with Biopython?

biopython python ncbi blast
• 2,881 views • link
written by ahtmatrix • ahtmatrix

Not an answer and just a comment. Legacy blast had a tool bl2seq which I still use a lot. It just aligns 2 sequences.

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written by microfuge microfuge

Agree with @WouterDeCoster: Doing a simple pairwise comparison can be easily done with the pairwise2 module of Biopython, like this: 

from Bio import pairwise2
....
alignment = pairwise2.align.globalxx(translated_protein, cds_to_protein, one_alignment_only=True)
print(pairwise2.format_alignment(*alignment[0]))

The module has several more possibilities to define gap penalties, score matrices etc.

• 0 views • link
written by Markus Markus

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