Difference between GenemarkS and getorf EMBOSS

Question

[Mimmi Ahlmén]

Hi!

I found a gene with GenemarkS that I didn't find with getorf EMBOSS. The start codon for this gene was GTG, so GenemarkS was able to find this gene just because it is a self-trained method? Which getorf EMBOSS is not? Is this the reason?

[Ram]

Genemarks is a gene prediction software. EMBOSS getorf does what its name says - it finds open reading frames (ORFs). You're comparing apples and oranges. Plus, looks like the codon usage dataset chosen/supplied is not equivalent between the two tools either.

[Mimmi Ahlmén]

What do you mean by different codon usage dataset? So getorf finds ORFs and GenemarkS genes? And this is why GenemarkS found this particular gene and not getorf?

[Ram]

What do you mean by different codon usage dataset

I'm venturing a guess that given genemarks looks a little more sophisticated than getorf, it might have a more expanded "codon table", whereas one might need to supply such an extended codon table to getorf.