[maker-devel] MAKER3 beta - EVM under predicting

[Tuan Duong Anh]

Dear MAKER-devel group

I have been testing out MAKER3 beta version and found out that EVM always
returns much less number of models. Did any one experience this before? I
do expect that EVM will return less models when compare to other, but not
to this extend (only 20% of the expected gene models). Any suggestion would
be much appreciated.

## Number of models obtained by each gene predictors:

HLIG.all.maker.augustus_masked.proteins.fasta:11224

HLIG.all.maker.evm.proteins.fasta:1974

HLIG.all.maker.genemark.proteins.fasta:11352

HLIG.all.maker.proteins.fasta:13672

HLIG.all.maker.snap_masked.proteins.fasta:13404

## maker_evm.ctl

#-----Transcript weights

evmtrans=10 #default weight for source unspecified est/alt_est alignments

evmtrans:blastn=0 #weight for blastn sourced alignments

evmtrans:est2genome=10 #weight for est2genome sourced alignments

evmtrans:tblastx=0 #weight for tblastx sourced alignments

evmtrans:cdna2genome=7 #weight for cdna2genome sourced alignments


#-----Protein weights

evmprot=10 #default weight for source unspecified protein alignments

evmprot:blastx=2 #weight for blastx sourced alignments

evmprot:protein2genome=10 #weight for protein2genome sourced alignments


#-----Abinitio Prediction weights

evmab=10 #default weight for source unspecified ab initio predictions

evmab:snap=7 #weight for snap sourced predictions

evmab:augustus=10 #weight for augustus sourced predictions

evmab:fgenesh=10 #weight for fgenesh sourced predictions

evmab:genemark=10 #weight for genemark sourced predictions



Regards,

Tuan
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