Optimizing Ublast

Question

[Juliofdiaz]

I am using the UBLAST tool from the USEARCH package by Edgar, and I am trying to shorten the time it takes to search for a large number of sequences in a large database. 95% of my sequences are found in a smaller subset of the database, whereas the rest needs the full database, which is much larger. So I was wondering if there is a way to print those sequences that were not found in the smaller database. After I would parse the output and ublast those reads to the larger database. Thanks

Answer 1

[Pavel Senin]

Can you use the -notmatched parameter? it suppose to generate FASTA file containing query sequences that did not match the database (Supported by v6.0.229 and later.) or weak hits, i.e. ‑weak_id?