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

[Fields, Christopher J]

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