[maker-devel] geneid (or alternative ab initio predictors)

[Sajeet Haridas]

One of the problems I have found with genemark is that it does not
understand a soft-masked genome. Hence, the self training is incorrect. I
have found marked improvement to genemark's prediction by running the
training on a hard masked genome.


On Mon, Mar 10, 2014 at 10:05 AM, Carson Holt <carsonhh at gmail.com> wrote:

> Adding a new predictor can take some time.  It obviously requires some
> coding.  It's usually not too hard just to convert results to GFF3 and
> then pass it in.  Integrated support is really only beneficial for
> predictors that can take "hints" from evidence alignments (for example we
> are working on EVM integration right now -
> http://evidencemodeler.sourceforge.net).  If SNAP and GeneMark give
> problems just drop them.  GeneMark really doesn't work very good on
> genomes with complex intron/exon structure (and I really wouldn't use it
> for anything but fungi).
>
> Make sure you are also giving sufficient protein evidence.  Perhaps all
> proteins from chicken and pigeon for example.  Then you shouldn't find
> loss of any true genes if just using Augustus.  Also try not to use gene
> count as an indicator of performance.  The value is very deceptive,
> especially if the genome assembly is fragmented.
>
> Thanks,
> Carson
>
>
>
> On 3/10/14, 8:52 AM, "Fields, Christopher J" <cjfields at illinois.edu>
> wrote:
>
> >I have been running MAKER 2.31 using Augustus and SNAP on an avian
> >genome.  Augustus gives pretty decent gene model predictions based on a
> >custom model we have and the hints MAKER provides.  However, SNAP seems
> >to throw out a ton of false positives; in many cases this appears to
> >cause erroneous gene fusions.  Leaving out SNAP altogether however leads
> >to a marked decrease in # models overall, which is worse.  GeneMark had a
> >very similar problem (high # false positives) and thus no marked
> >improvement, either when using with both Augustus and SNAP or with
> >Augustus alone.
> >
> >I have been exploring using geneid
> >(http://genome.crg.es/software/geneid/) as an alternative, based on some
> >feedback on another project I worked with int he past.  This would be
> >feed into MAKER using external GFF, but I wanted to see if anyone has
> >tried geneid with MAKER first.
> >
> >Finally, how hard would it be to incorporate alternative callers into
> >MAKER?  For instance, would it be possible to add these like a 'plugin'?
> >
> >chris
> >_______________________________________________
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>
>
>
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