[maker-devel] Effect of the unmask option

[Carson Holt]

The unmasked option allows the ab initio predictions ran on unmasked
sequence to compete against other models, and only if they have a better
AED score are they selected.  They are not available for non-overlapping
rejected models at the end of the run because that set is non-redundant
and they tend to have a very high likelihood of being transposons
themselves.  So I don't let a repeat containing model override a
non-repeat containing model unless there is evidence supporting it (there
is noever evidence supporting the non-overlapping models).

--Carson


On 13-06-06 4:44 AM, "Michael Nuhn" <mnuhn at ebi.ac.uk> wrote:

>Hello Carson!
>
>When running maker with the unmask option, how does maker use the
>predictions generated from running the gene predictors on the unmasked
>sequence?
>
>The tutorial says:
>
>"You do have the option to run ab initio gene predictors on both the
>masked and unmasked sequence if repeat masking worries you though. You
>do this by setting unmask:1 in the maker_opt.ctl configuration file."
>
>http://gmod.org/wiki/MAKER_Tutorial_2012
>
>But in the sub get_non_overlaping_abinits in maker::auto_annotator
>(maker version 2.27) they are skipped:
>
>#only accept masked predictions unless I'm not masking or the predictor
>is genemark
>my $src = $g->{algorithm};
>unless($src =~ /_masked$|^pred_gff/ || $CTL_OPT->{_no_mask} ||
>$CTL_OPT->{predictor} eq 'genemark') {
>	   next;
>}
>
>Cheers,
>Michael.
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org