extract viral protein of interest from 10k whole viral genomes

Question

[Shwetha]

I have 10k whole viral genome sequences, and I want to extract one viral gene sequence from each of these whole genomes.

Currently, I am using nBLAST with required gene as query and a subject of max 300 whole genome sequences.

Since BLAST has a 10,000,000 letter limit, I am unable to process all 10k sequences at once.

Is there a way to bypass using BLAST with some other tool? Or a way to expand the character limitation of BLAST?

[GenoMax]

With a large dataset it is always best to do the search locally (or in the cloud, if you don't have necessary hardware available locally).