text: user9373: 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?
  
  user2970: 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.
  
original_text: 9373: <p>I have an assembly of an algae and want to find if it has anything analogous to endogenous retroviruses' subsequences in its DNA.</p>
  <p>My guess is I should manually blastn all subsequences until I find (or not something) that could have come from a virus.</p>
  <p>Is there a better way to do this?</p>
   2970: <p>Your guess sounds reasonable to me but you should consider using <a href="https://github.com/DerrickWood/kraken2/wiki/Manual" rel="nofollow noreferrer">KRAKEN2</a>. 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.</p>
  