[maker-devel] [Maker] Gene density threshold?

[Carson Holt]

There is no gene density parameter, and for gene overlap there is no distance parameter. Gene overlap on the same strand is not permitted though. If a gene is being excluded because of UTR overlap, you can someone correct for that by setting correct_est_fusion=1. That will trim back the UTR on those cases since this type of exclusion is often caused by false merging of neighboring transcripts during mRNA-seq assembly. Some organisms like fungi do truly have UTR overlap observed some genes, but mRNA-seq reads will assemble into a single transcript, so it’s hard to tease apart. Trimming back the UTR in those cases tends to be the most reliable solution.

—Carson


> On Dec 7, 2017, at 9:13 AM, Jeanne Web <jeanne.wilbrandt at web.de> wrote:
> 
> Dear MAKER developers,
> 
> I have wondered whether there is an internal threshold or cutoff value for gene density (allowing only x genes in a genomic region of a certain size) or gene overlap (requiring to be predictions x bases apart from each other)?
> 
> We have come to this idea when re-annotating a genome with another gene predictor. Several cases of single-exon genes not predicted by MAKER but flanked (i.e. close proximity) by MAKER-predictions were observed.
> 
> Thus, I'd like to ask: Which factors (apart from sequence/signals and evidence/AED) influence the algorithmic prediction decision?
> 
> Any help is highly appreciated.
> With best wishes
> Jeanne Wilbrandt
> 
> 
> ~~~
> Jeanne Wilbrandt, M.sc.
> ORCID 0000-0002-0363-3837
> ~~~
> PhD candidate
> Leibniz PhD representative, student representative
> Leibniz Graduate School on Genomic Biodiversity Research
> ZFMK ~ zmb ~ University of Bonn
> 
> 
> 
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