Here's the situation.
I have proteome files for a bunch of strains. Each strain has its own fasta proteome (strain1.faa, strain2.faa, strain3.faa).
I also have a fasta list of AA sequences, and I want to know if they are present within these strains. That "query" file, looks like this:
What I want in the end is a matrix with the strains in first column, and first row being the genes. I DONT want to have to do a manual blast for every cell because that's impractical. I just want the information. The values in the matrix is the %identity of that gene in that strain. It will look like this: What is the most parsimonious way to go about this project? I have a lot of strains, and hundreds of genes to test. But, I'm okay with outputing a csv for now. It's such a large task that I'm unsure of how to start it.