step-by-step scripts for the example data

[BinhongLiu]

Hi,
I'm trying to test the spacedust to figure out the conserved gene clusters between the two example genomes.

1. Creating databases
   spacedust createsetdb listOfFastaFiles.tsv setDB tmpFolder --gff-dir examples/gff.txt --gff-type CDS

the listOfFastaFiles.tsv is:
examples/uvig_120081.fna
examples/uvig_255655.fna

2. Convert to structure sequence DB (the reference FoldseekDB Alphafold/UniProt has been downloaded in ~/database/FoldSeek/UniProt/ and named as afdb.
   spacedust aa2foldseek setDB ~/database/FoldSeek/UniProt/afdb tmpFolder
   Here I got two databases, setDB_foldseek and setDB_unmapped.
   Q: I will analyze some virus genomes later, so full Foldseek structure searches against precomputed structures probably is a better choice than ProstT5?

3. Search querySetDB against targetSetDB (using Foldseek and MMseqs)
   spacedust clustersearch setDB setDB result.tsv tmpFolder --search-mode 1 --num-iterations 2

4. I got the result.tsv file here.

result.tsv

I am not sure whether I have run the tool correctly. I am also confused by the results, as I would expect to observe some conserved gene clusters between the two example genomes.

Q: Besides, what if I have many genomes and want to identify the conserved gene clusters between any of the genomes?

Thanks!
Best wishes!