[Question] Paper doesn't mention fungal genomes--any reason it shouldn't work?

[DaRinker]

Just wanted to hear from the developers why they didn't explicitly mention fungal genomes in the Nature Methods paper?

Just an oversight, or is there something about the intergenic/intronic nature of eukaryotic genes that makes it more difficult (because I can't see any)

Thanks

[DaRinker]

And I see this:

"Note: this only works with (prokaryotic) genomes without intron/exon structures or (2) FASTA (.faa or .faa.gz) files of protein sequences with header format from Prodigal.

So I see I would at leasts need to spoof the header format somehow,...

[RuoshiZhang]

Hi! You are right: Spacedust is able to process fungal genes as long as they are already translated into protein sequences, and the positions should be parsed from the prodigal-like header. We didn't explicitly advertise this mostly because we didn't present any examples of use in fungi/eukaryotes in the paper.