An E-value threshold must be specified.
The -strand option is required for nucleotide databases.
Nucleotide, protein and translated searches are supported.
The -accel option tunes search speed against sensitivity. Smaller values are faster but tend to have lower sensitivity to hits with lower sequence identity. Default is 0.8. See UBLAST algorithm for more discussion.
Weak hits (Weak hits are especially useful with ublast)
usearch -ublast reads.fasta -db proteins.udb -evalue
1e-9 -accel 0.5 -alnout results.aln