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

[Carson Holt]

We can look into it.

—Carson

From:  "Fields, Christopher J" <cjfields at illinois.edu>
Date:  Thursday, March 13, 2014 at 3:04 PM
To:  Sajeet Haridas <sajeet at gmail.com>
Cc:  Carson Holt <carsonhh at gmail.com>, "<maker-devel at yandell-lab.org> List"
<maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] geneid (or alternative ab initio predictors)

That is nice to know; I’ll have to check the masking on this assembly to see
if that is the problem (my guess is that it is).

Carson, re: geneid and ‘hints’, it looks as if geneid can take some hints
such as BLAST HSPs (as well as other information), in the form of a GFF
‘homology’ file.  I assume it could take protein2genome/est2genome as well
through the same route.

chris

On Mar 10, 2014, at 1:31 PM, Sajeet Haridas <sajeet at gmail.com> wrote:

> 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
>> <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
>>> >_______________________________________________
>>> >maker-devel mailing list
>>> >maker-devel at box290.bluehost.com
>>> >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
>> 
>> 
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> 



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