[maker-devel] missing start and stop codons

[Carson Holt]

They are incomplete genes there are many reasons why this happens in new
assemblies.  You can turn always_complete on to try and force a complete,
but what is added or subtracted to get a start and stop codon may not be
biologically correct.  It's just forced canonical.  Also make sure to use
the latest MAKER version.  2.29 and before didn't correct for the BioPerl
codon table which allows for an extra non-cannonical start codon.  Now MAKER
exports a strict canonical table to BioPerl so 'M' is the only start.

--Carson


From:  "Mack, Brian" <Brian.Mack at ARS.USDA.GOV>
Date:  Thursday, June 5, 2014 at 11:56 AM
To:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  [maker-devel] missing start and stop codons

I’ve been looking at the start and stop codons of the maker predicted
transcripts after I stripped off the utr with the fasta_tool script and 7%
of the transcripts do not have ATG as a start codon. Also 2% do not have
TAA, TAG, or TGA as a stop codon. Could these be real start and stop codons
and just rare variants, or should I consider these incomplete genes? If I
was to turn on the “always_complete” option in Maker what would that
actually do? 
 
Thanks,
Brian




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