[maker-devel] About split genes in MAKER annotation

[Carson Holt]

It’s best to look at these in a browser like Apollo where you can also manipulate the intron/exon structure. What you will often find is that there is something that breaks the ORF or breaks splicing, so the predictors can’t build an end to end model even with the hints given. If you have a GFF3 just for the contig, I can also look at it in a browser to help point out the logic that lead to the model.

—Carson

> On Dec 12, 2018, at 3:29 AM, Prashant Narendra SHINGATE <prashantns at imcb.a-star.edu.sg> wrote:
> 
> Hi Carson,
>  
> I am Prashant a Bioinformatics postdoctoral fellow from Prof B Venkatesh’s lab, IMCB, A*STAR. I am using MAKER-tool to annotate an invertebrate genome (~2Gb). During annotation process, we found several instances of split geneseven though we have full-length reference protein sequences from very closely related species. Hence we decided to look at one of the loci to understand the reason behind it and to optimize the parameters.
>  
> We looked at a gene ~110kb long and codes for a ~1200 amino acid protein. We have a highly identical reference protein (>90% identity and 100% coverage) from another species. In addition we also have a high coverage Trinitytranscript assembly from our species. Still, this gene is split into 4 fragments during evidence-based MAKER run. On closer a look, we found that the above mentioned closely related protein is not aligned by exonerate (protein2genome) even though it is the closest protein to this gene in our dataset. It looks like the program is giving more weightage to transcripts which are typically fragments of the gene. So we are at a loss as to how to predict this gene in full.
>  
> For your reference, I am herewith enclosing maker_opts.ctl file and maker_bopts.ctl. I will be glad to share the scaffold sequence and other input files if required.
>  
> Can you please help me to understand the reason behind MAKER not able to use the full-length reference protein for gene prediction and how we can overcome this problem.
>  
> Thanks for your time and help.
>  
> Best regards,
>  
> Prashant Shingate, PhD <mailto:prashantns at imcb.a-star.edu.sg> :: Research Fellow :: Comparative and Medical Genomics Lab :: Institute of Molecular and Cell Biology (IMCB) :: Agency for Science, Technology and Research (A*STAR)
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> <maker_opts.ctl><maker_opts.ctl>

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