[maker-devel] (no subject)

[Panos Ioannidis]

I got back to my annotations this past week and have a couple of questions!

1) Since my organism isn't closely related with any other that's already
sequenced, I will have to run maker twice (according to the tutorial). So
for the first run I see that some people use only the ESTs and some others
use ESTs and a protein database (CEGMA, Uniref50, Swiss-Prot, etc). I guess
that the ESTs will give better models, but for the cases where genes aren't
covered by an EST, it's okay to have a protein database to detect them as
well. Am I right? What do you think?

2) In case I use both ESTs and a protein database how should I set the
est2genome and protein2genome parameters in the maker_opts.ctl file? Should
they both equal to "1"?

3) I've been thinking of running the BLAST searches separately and giving
Maker directly the results. I guess that in this case, I'll have to first
convert the BLAST output to a gff3 file and give it to the protein_gff
parameter, right?

Thanks,
Panos
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