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

[Jeanne Web]

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