even though I've used BLAST for various things in the past, I've encountered a problem, that I could not solve myself.
I've a list of taxid's or organism names with complete genomes (n=400) and a gene sequence/protein sequence (roughly 450 AS/ 1500 nt) from my model organism. I want to retrieve the most similar hits of this gene sequence in each of the 400 genomes. How can I do that online or by using a Biopython script?
I know, that I can restrict a BLAST search to one or up to 20 genomes using the NCBI website, but not more than that.