An E-value threshold must be specified.
A database file must be specified using the -db option. FASTA and .udb formats are supported. For large databases, .udb format is recommended (see makeudb_ublast command).
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.
See also
Output files
Accept options
Weak hits (Weak hits are especially useful with ublast)
Termination options
Indexing options
Multithreading
Masking options
Alignment parameters
Alignment heuristics
Example
usearch -ublast reads.fasta -db proteins.udb -evalue
1e-9 -accel 0.5 -alnout results.aln