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nextgenusfs / funannotate

Eukaryotic Genome Annotation Pipeline
http://funannotate.readthedocs.io
BSD 2-Clause "Simplified" License
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duplicated genes and protein evidence #824

Open caonetto opened 1 year ago

caonetto commented 1 year ago

Hi, I have been wondering, how does funannotate deal with gene duplications when supplying protein evidence? Ive noticed that diamond doesn't seem to allow multi mapping and therefore only one of the genes gets the protein support.

Thanks.

hyphaltip commented 1 year ago

protein support is only one part of evidence fed to the gene prediction software, there will also be de novo predictions made without the help of evidence. I am not sure if we want to support alternative placement for paralogs in the alignment step but might have to test and see. So I think this is just a factor of whatever alignments diamond produces. The magnitude of how much this impacts your predictions of paralogs if you do or don't have transcript support as well.