Our lab has sequenced a set of different Bacillus strains and assembled contigs for each individual genome. I wish to set up a search for the presence/absence of multiple known genes (we have FASTA files for those) in our set of genomes. I was hoping to do this via BLAST but looking at the website, it seems that you can only search for genes in genomes exclusively available on the NCBI database.
Is there any way to set up a search for genes in the genomes of the strains that I've sequenced and assembled? I was hoping to find an option to upload our own "search sets" but it doesn't seem to be available on http://blast.ncbi.nlm.nih.gov/Blast.cgi