[maker-devel] Query on genemark results

[kokwei]

Hi,

I have the same problems as posted by André Gomes on 10/4/10. I still
have the same problems even though using the current available version
of maker (maker 2.1 and maker 2.26 beta version).

I have tried to do the gene prediction on eukaryotic genome using 3
ab-initio gene predictors (SNAP, Augustus and GeneMark-ES) using Maker.
From the fasta_merge output, I have 3 separate files of gene models
($prefix.all.maker.augustus_masked.proteins.fasta,
$prefix.all.maker.snap_masked.proteins.fasta and
$prefix.all.maker.genemark.proteins.fasta) and one
$prefix.all.maker.proteins.fasta (I presume this should be the consensus
gene models from 3 predictors' results, right?).

From the consensus gene models file, I don't see even one result from
genemark but all from snap/augustus only. Is that normal?
Also from the file naming and gene model label in final gff file, it's
showing that genemark is not masked like those of augustus and snap? Is
that true? Why only augustus and snap masked but not genemark? Please
assist and thanks for your helps.

Kok Wei




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