Transdecoder with custom genetic codes?

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marcus Senra

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Apr 2, 2021, 10:56:53 AM4/2/21

to TransDecoder-users

Hi,

I'm studying organisms with different codon reassignments, mostly within their stop codons, in which, in many cases, are not the ones available in -G list. Is there a way to run transdecoder with custom genetic codes? Is it possible (easy) to modify the code to allow this?

Thanks

Marcus

Brian Haas

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Apr 2, 2021, 12:23:20 PM4/2/21

to marcus Senra, TransDecoder-users

Hi Marcus,

All the logic for translating according to genetic code is here:

https://github.com/TransDecoder/TransDecoder/blob/master/PerlLib/Nuc_translator.pm

You could hack it to add something additional if it's not already represented.

best,

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