Question: Maker Genome Annotation - protein isoforms
gravatar for luca
13 months ago by
luca30 wrote:

Hi everyone, Just a quick question. I am learning how to annotate genomes using maker (

As a test, I downloaded Chromosome 2 of the fish Cottoperca gobio in fasta format, downloaded from NCBI here ( I managed to run maker and output the proteins from maker with the command:

gffread yourgenome.maker.all.gff -y yourgenome.pep.fasta -g yourgenome.sequence.fasta

I am checking the goodness of my assembly by comparing my .gff file with the .gff from NCBI using JBrowse and noticed that my maker run has one peptide sequence per one gene. In other words, for each gene in my chromosome I have only one protein, and I do not have proteins from alternative splicing (that are to be expected in a normal vertebrate genomes). So I was wondering, how do I obtain these proteins from alternative splicing in my genome? Is maker only considering/creating one protein per gene on purpose?

Thanks for your help, Best regards Luca

maker annotation genome • 435 views
ADD COMMENTlink modified 13 months ago • written 13 months ago by luca30

Thanks for the reply Juke. I found the option and I will give it a go with the option enabled.

Thanks again Luca

ADD REPLYlink written 13 months ago by luca30

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized. This comment belongs under @Juke-34's answer.

SUBMIT ANSWER is for new answers to original question.

ADD REPLYlink written 13 months ago by genomax92k
gravatar for Juke34
13 months ago by
Juke344.9k wrote:

Yes there is an option for isoforms. Re-run MAKER with the option activated in maker_opt.ctl

ADD COMMENTlink written 13 months ago by Juke344.9k
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