[maker-devel] Cryptic ACG start codon

[Carson Holt]

MAKER uses the is_start_codon method from Bio::Tools::CodonTable to determine if a codon is a valid start codon.  Right now I don’t have a way to swap out the codon table. There is a way to do it, but it’s not easy.

If you edit …/maker/lib/CGL/TranslationMachine.pm line 122, you can set the table id to be another one from the BioPerl docs —> http://doc.bioperl.org/releases/bioperl-1.6.1/Bio/Tools/CodonTable.html#BEGIN1 <http://doc.bioperl.org/releases/bioperl-1.6.1/Bio/Tools/CodonTable.html#BEGIN1>

Or you can manually add your own codon table.  It won’t change the codon usage for aligners like BLAST and Exonerate, but if will allow you to specify another valid start codon.

To do that, edit line 118 to add your own manual codon table my adding another ‘M’ below the position you want to make into a valid start codon.

        my $id = $self->add_table(
            'Strict',
            'FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
            '-----------------------------------M----------------------------');
        $self->id($id);

I don’t really know which string position goes with which three letter nucleotide code.  You might have to reverse engineer that from the BioPerl docs in the link above.

—Carson


> On Jul 21, 2015, at 1:10 PM, Shaun Jackman <sjackman at gmail.com> wrote:
> 
> Hi, Carson.
> 
> I’m working with a plant mitochondrial genome that has a lot of C to U RNA editing. One effect of this editing is that AUG start codons can be created by editing ACG to AUG. Does MAKER have any particular support for cryptic start codons?
> 
> I’m using protein evidence (protein and protein2genome), and a number of the protein sequences that I downloaded from Genbank start with a - character, which indicates a ACG start codon. It would fantastic if - were allowed to match either ACG or ATG in the genome.
> 
> Cheers,
> Shaun
> 
> 
> 
> 
> -- 
> http://sjackman.ca/ <http://sjackman.ca/>
> 
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