[maker-devel] evidence for MAKER vs evidence to train gene finders

[Steven Sullivan]

Thanks! So, I think for training the gene predictors, I'll try to identify
any sequences in my gold-standard set that have structural in
information...i.e. genes for which the genomic sequence was cloned....and
use those.  But  I doubt there's enough of those to train e.g. Augustus, so
I'll probably have to use the bootstrap method as well . Is there a way to
combine both?

For the BLAST-based annotation, if I use entire Uniprot/Swissprot or
Genbank FASTA sets as protein homology evidence , my gold standards are
already included in those.  I gather from these replies that that's not a
problem.

However, there *are* public database sequences (predicted genes from an
older annotation of this species) that I *do* want to exclude from
evidence.  (Because we want to run MAKER as if this genome was 'new', never
before annotated.)  Can I use something  like the -negative_gilist  option
in blastp , to omit previous genome project predictions from consideration?
 (An  option that only works with Genbank sequences, I think) .  Or do I
have to create a  custom version of the large public database?
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