BLASTing long sequence

Question

[igor]

I have a long sequence (1-5 MB). I am trying to BLAST it using web-based NCBI BLAST against the nt database to see if it's a known organism. It works with megablast (highly similar sequences), but the results aren't great. If I try discontiguous megablast or blastn, it crashes. Is that a known issue? Would running BLAST locally solve that? Is there an alternate solution (I would prefer not to download the entire nt database)?

Answer 1

[Ram]

You can run BLAST locally and still have it use the nt database from NCBI with the -remote option as mentioned here: https://www.ncbi.nlm.nih.gov/books/NBK279680/