[maker-devel] question regarding alternate splicing annotation

[Carson Holt]

Using GFF3 pass-through options alone won't allow for the alternate splice
prediction to work.  You have to also allow gene predictors like SNAP and
Augustus to run.  MAKER uses mutually exclusive EST data to produce separate
hint files in some cases that can produce alternate splice forms from the ab
initio predictors.  The EST evidence must be very long in general or they
will not produce alternate forms.  These alternate splice model can then
compete against your existing gene models based on scoring statistics MAKER
produces and potentially replace them.  This may not be what you want
though.  The alternate splice prediction works better De Novo than for
re-annotation.

The alternate splicing option still needs more work, but I would appreciate
any feedback.

Thanks,
Carson




From:  Walter Eckalbar <weckalba at asu.edu>
Date:  Monday, 4 June, 2012 1:41 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] question regarding alternate splicing annotation

Hi Maker developers,

I am trying to expand on some current annotations that are already quite
good, but only predict protein coding sequence and one isoform per gene, to
add UTRs and alternative splice forms from cufflinks data.  To do this I put
the current annotations in both the model_gff andusing the gff_field, plus
the cufflinks gff3 for the ests (as I noticed was suggested in a previous
email).  I've left everything else as default, except changing alt_splice=1.
I am watching the progress of the *.gff.ann files, but I'm not noticing
alternate splicing being added, while UTRs are being picked up (exons being
added, etc.).  This is a vertebrate genome, so run times are fairly long and
I just wanted to double check if I wasn't missing something.  Will maker go
back through a second step to annotate alternative splicing?  Or should I be
trying something a little different.

Thanks,

Walter
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