If you convert it to standard GFF3 format, MAKER will take it as input. GlimmerHMM would go into the pred_gff option.
From: ckuanglim <[hidden email]> Date: Friday, 13 July, 2012 3:01 AM To: Carson Holt <[hidden email]> Subject: Re: [maker-devel] adding a new gene predictor to maker 2
Can I pass the output from GlimmerHMM into MAKER?
On Friday, July 30, 2010 9:43:53 AM UTC+8, Carson Holt wrote:
mRNA-seq data can be passed to MAKER by first processing the data and then putting it into GFF3 format, i.e. process with something like tophat and cufflinks and then convert the
output into GFF3. MAKER comes with tophat2gff3 and cufflinks2gff3 conversion scripts. Supply the results to the est_gff option in the maker_opt.ctl file. For ab initio gene predictors, do the same. Convert the output into GFF3 format then supply the data
to pred_gff in the maker_opt.ctl file. Using GFF3 pass-through you can supply MAKER with evidence from virtually any external source of your choice. You just have to convert it into GFF3 so MAKER understands how to use it.