Codon Alignment Via Python?

Question

[a1ultima]

I have pairs of coding DNA sequences which I wish to perform pairwise codon alignments via Python, I have "half completed" the process.

So far..

• I retrive pairs of orthologous DNA sequences from genbank using Biopython package.
• I translate the orthologous pairs into peptide sequences and then align them using EMBOSS Needle program.

I wish to..

• Transfer the gaps from the peptide sequences into the original DNA sequences.

Question

I would appreciate suggestions for programs/code (called from Python) that can transfer gaps from aligned peptide sequence pairs onto codons of the corresponding nucleotide sequence pairs. Or programs/code that can carry out the pairwise codon alignment from scratch.

[Rm]

check for some insights in coding for codon alignment http://zruanweb.com/

[Andrzej Zielezinski]

Don't reinvent the wheel unless you simply like creating wheels:) Use: http://translatorx.co.uk/ If you still want to do this in Python, paste some of your code, we will make this work.

[Asaf]

This sounds like a simple loop iterating each sequence of the proteins, writing three letters from the DNA if not a gap and three gaps if it is. This is assuming you're in-frame.

[a1ultima]

cheers, in the end I did something like that eventually and posted the answer to my own question

[Damian Kao]

Are your DNA sequences already in the correct frame?

Answer 1

[a1ultima]

In the end I made my own Python function that transfers gaps ('-') from the peptide sequence to the nucleotide sequence (codons).

It takes an aligned peptide sequence with gaps and the corresponding un-aligned nucleotide sequence and gives an aligned nucleotide sequence:

Function

def gapsFromPeptide( peptide_seq, nucleotide_seq ):
    """ Transfers gaps from aligned peptide seq into codon partitioned nucleotide seq (codon alignment) 
          - peptide_seq is an aligned peptide sequence with gaps that need to be transferred to nucleotide seq
          - nucleotide_seq is an un-aligned dna sequence whose codons translate to peptide seq"""
    def chunks(l, n):
        """ Yield successive n-sized chunks from l."""
        for i in xrange(0, len(l), n):
            yield l[i:i+n]
    codons = [codon for codon in chunks(nucleotide_seq,3)]  #splits nucleotides into codons (triplets) 
    gappedCodons = []
    codonCount = 0
    for aa in peptide_seq:  #adds '---' gaps to nucleotide seq corresponding to peptide
        if aa!='-':
            gappedCodons.append(codons[codonCount])
            codonCount += 1
        else:
            gappedCodons.append('---')
    return(''.join(gappedCodons))

Usage

>>> unaligned_dna_seq = 'ATGATGATG'
>>> aligned_peptide_seq = 'M-MM'
>>> aligned_dna_seq = gapsFromPeptide(aligned_peptide_seq, unaligned_dna_seq)
>>> print(aligned_dna_seq)

    ATG---ATGATG

[Andrzej Zielezinski]

+1 for sharing it