[maker-devel] Alternative start codons

[Fields, Christopher J]

We had a user notice that MAKER is not observing alternative start codons for bacterial genomes.  For instance, this predicted transcript:

>Xf_Mul_000007-RA transcript Name:"Protein of unknown function" offset:79 AED:0.42 eAED:1.00 QI:79|-1|0|1|-1|1|1|20|24
GTGGGATACAGGCCGCTGATCGCTGATGGCGCGTACCTGAAACTGCTGCTGGACTACTAC
GTTACAGTGCAGCCTTTGCATGCCGATTGGAAAGATCTATATATCATCGCTTGCGCTATT
ACAGCGGCTAAAAAGAGTCTTCAATTTGGCGTAATTCAGTCATTGGCGGGGTAG

Yields this protein sequence.

>Xf_Mul_000007-RA protein AED:0.42 eAED:1.00 QI:79|-1|0|1|-1|1|1|20|24
MPIGKIYISSLALLQRLKRVFNLA

I'm pretty sure I know what is going on, namely that MAKER is treating the 5' end as UTR and looking for the first ATG (there is one in the sequence above).  Is there any way to change this behavior, though?  For instance, allow alternative start codons like GTG/TTG?

chris