I have a hard time solving a relatively simple problem (I am a novice)
I want to screen a collection of >8000 Prokaryot genomes for at specific gene, in order to make an prescence/absence table for a GWAS study. However, I am not sure how to go about this. I have the sequence of the gene in FASTA format, as well as all the genomes. Could I perhaps use Blast+ and create a local database of the genomes? I have the genomes as fna files directly from GenBank but I also have annotated versions from running Prokka.
Thank you in advance!