[maker-devel] Cryptic ACG start codon

[Shaun Jackman]

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/
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