I am looking for some virulence factors in aeromonas genomes. I use abricate and VFDB yet I can’t find what I need (I know the genes are present as the samples are PCR positive and I also found them in the asseblate using blast). I don’t understand why I can’t find them with abricate (this is one of the genes in question VFDB - aerA/act gene (VFG038892)). I also tried using abricate with a reference genome that I know for a fact contains the gene. I thought that maybe it was not present in VFDB but in the publications it is used without problem for those genes.
What am I not seeing? thanks
Have you tried to visualize the assembly and annotation in a genome browser? IGV would be a good choice for this.
Some of these tutorials are still in development (we are working to incorporate IGV directly into Galaxy) but you can use it as a stand-alone application from your own computer, and load files through Galaxy if the database (genome) metadata is set up. Or, download the files and upload directly. I also added a tag to this topic that will link to prior topics with how-to-use help.
Let’s start there