How to find possible viral subsequences in a Eukaryote genome? I have an assembly of an algae and want to find if it has anything analogous to endogenous retroviruses' subsequences in its DNA.
My guess is I should manually blastn all subsequences until I find (or not something) that could have come from a virus.
Is there a better way to do this?
Your guess sounds reasonable to me but you should consider using KRAKEN2. You can create your custom database (you would have done it with makeblastdb anyway) and kraken will check k-mers against the database to find homologous sequences.