[Bioperl-l] Amino Acid sequence to nucleotides sequence

Fields, Christopher J cjfields at illinois.edu
Mon Apr 16 16:44:21 EDT 2012


On Apr 16, 2012, at 3:32 PM, Peter Cock wrote:

> On Mon, Apr 16, 2012 at 9:08 PM, shalu sharma <sharmashalu.bio at gmail.com> wrote:
>> Hi All,
>>            Is there any way in Bioperl i can convert amino acid sequences
>> to nucleotide sequences.
>> 
>> Thanks
>> Shalu
> 
> Probably - but there is more than one answer since the codon
> tables are a many-to-one mapping. Are you hoping for one
> possible nucleotide sequence, perhaps with IUPAC ambiguity
> characters? Perhaps a specific example of what you want
> would help - back-translation is a fuzzy term.
> 
> If you are trying to combine a protein alignment with the
> original unaligned nucleotide sequences to make a codon
> alignment that's a different task.
> 
> Peter

We do have a revtranslate function in bioperl that is supposed to deal with ambiguities:

https://metacpan.org/module/Bio::Tools::CodonTable#revtranslate

I don't know how well-tested it is, but it was added a few years back to Bio::Tools::CodonTable.  IIRC Mark Jensen was the developer who did that, and he's pretty meticulous.

chris




More information about the Bioperl-l mailing list