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!
Question: Translating Nucleotide MSA to Amino Acid MSA
5.2 years ago by
weslfield • 90
weslfield • 90 wrote:
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5.0 years ago by
Whetting • 1.5k
Whetting • 1.5k 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 SeqIOwith 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)
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