Return a list of codons from a sequence

ryan — Thu, 10 Jan 2008 15:44:57 +0000

There are no built-in functions (that I know of) for returning a list of codons from a sequence, but making your own is quite simple. This function is from Solution A.5 from the Python Course in Bioinformatics


def codons(s, frame=0):
    """Return a list of codons from a string, s, giving an optional frameshift."""

    codons=[]

    end=len(s[frame:]) - (len(s[frame:]) % 3) - 1

    for i in range(frame,end,3):
        codons.append(s[i:i+3])

    return codons

A quick codon table

ryan — Thu, 06 Dec 2007 02:40:25 +0000

Sometimes it’s nice to be able to have a codon table handy. Rather than typing out one by hand, theTranslate module contains the codon table of your choice in dictionary form:

from Bio import Translate
translater=Translate.unambiguous_dna_by_id[11]
bacterial_table=translater.table.forward_table

Note 1: See the NCBI Translation Tables for the correctid number to use for your sequence.

bacterial_table['TAT']
>>>'Y'

And here’s how to easily reverse it, where the keys are amino acids and the values are lists of codons:

back_table = {}
for key,value in bacterial_table.iteritems():
    try:
        back_table[value].append(key)
    except KeyError:
        back_table[value]=[key]

scienceoss.com » codons

Return a list of codons from a sequence

A quick codon table