[BioPython] Inverse codon table?
Peter
biopython at maubp.freeserve.co.uk
Tue Aug 14 17:17:31 UTC 2007
Sebastian Bassi wrote:
> I am looking for a table in Biopython of amino-acids and its codons. I
> found in Data.CodonTable a table but it should be used in the inverse
> way I need:
>
>>>> from Bio.Data import CodonTable
>>>> t=CodonTable.standard_dna_table
>>>> t.forward_table["ATG"]
> 'M'
>
> I need a table that I coulld enter "M" and get the all triples that
> translate into "M". Is this available in Biopyhon?
>
I'm not sure without a thorough check, but its fairly be trivial to
build such a dictionary from the CodonTable.standard_dna_table like this:
from Bio.Data import CodonTable
t=CodonTable.standard_dna_table
t.forward_table["ATG"]
#Build a back table dict where the values are lists of codons...
bt = dict()
for a1 in "ATCG" :
for a2 in "ATCG" :
for a3 in "ATCG" :
codon = a1+a2+a3
try :
amino = t.forward_table[codon]
except KeyError :
assert codon in t.stop_codons
continue
try :
bt[amino].append(codon)
except KeyError :
bt[amino] = [codon]
for amino in bt :
print amino, bt[amino]
Peter
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