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ublast command
Sensitive database search using the UBLAST algorithm. Alignments are local.

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 search flowchart for overview of searching in USEARCH commands.

See also
  Output files
Accept options
  Weak hits (Weak hits are especially useful with ublast)
  Termination options
  Indexing options
  Masking options
  Alignment parameters
  Alignment heuristics


usearch -ublast reads.fasta -db proteins.udb -evalue 1e-9 -accel 0.5 -alnout results.aln