Question: Translating Nucleotide MSA to Amino Acid MSA
1
gravatar for weslfield
6.2 years ago by
weslfield90
European Union
weslfield90 wrote:

Hi, so I have a nucleotide mutliple sequence alignment that I would like to translate into an amino acid MSA based on the reading frame of a reference sequence in that alignment. Looking for the best way to do this, preferably a Biopython way. Thanks!

msa sequence alignment • 2.1k views
ADD COMMENTlink modified 5 months ago by mrinsmrids0 • written 6.2 years ago by weslfield90

Why is it better to translate a nucleotide sequence to an amino acid sequence for MSA?

ADD REPLYlink written 5 months ago by mrinsmrids0

DNA codons can are redundant, amino acids are not.

ADD REPLYlink written 5 months ago by ATpoint38k
1
gravatar for Whetting
6.0 years ago by
Whetting1.5k
Bethesda, MD
Whetting1.5k wrote:

not sure you are still interested but...this solution assumes that the nucleotide alignment is a codon alignment. If not, you will end up with a bunch of "X" as aminoacid

from Bio import SeqIO

with open("translated.fas","w") as out:
    for record in SeqIO.parse("alignment.phy","phylip"):  ##change this to whichever format
        sequence=[]
        for c in range(0,len(record.seq),3): change to 0, 1, 2 depending on the frame of the reference
            codon = record.seq[c:c+3]
            if "-" not in str(codon):
                sequence.append( str(codon.translate()) )
            elif str(codon)=="---":
                sequence.append( "-" )
            else:
                sequence.append( "X" )
        print >>out, ">"+record.id
        print >>out, "".join(sequence)

 

           

 

ADD COMMENTlink modified 6.0 years ago • written 6.0 years ago by Whetting1.5k
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