[maker-devel] ATG strict start codon usage query

[Carson Holt]

Make sure you are using the latest maker version (2.31.8 - since about 2014). Make sure you are not using GFF3 files as input to MAKER (otherwise you will use whatever codon is in the GFF3 ). Make sure your BioPerl is up to date (CPAN version not BioPerl live version). With respect to behavior, MAKER by default will keep whatever start codon given used by the ab initio predictor, and only search for a different one if you set always_complete=1.

—Carson



> On Oct 6, 2016, at 5:30 AM, Robert King <robert.king at rothamsted.ac.uk> wrote:
> 
> Hi,
>  
> I’m using latest version of Maker2 but when I use it I get CTG and TTG as start codons of which I don’t want. Reading threads, the bioperl CodonTable.pm has been changed to allow for strict setting so that only ATG is used. My question is how to invoke this functionality? I’ve looked in maker ctrl files and command line maker but don’t see how to get it just to use ATG as the start codon. Can you please advise.
>  
> Best wishes
> Rob
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