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search_local command
Comprehensive database search. All database sequences are aligned to the query, no index is used. Alignments are local. Much slower than usearch_local or ublast for large datasets; mostly useful for ad hoc queries on small datasets. A hit will be found only if there is at least one exact matching word of length -hspw, which defaults to 3 for proteins and 5 for nucleotides, or the ‑fulldp option is specified (see alignment heuristics).

An E-value threshold must be specified using the ‑evalue option.

A database file must be specified using the ‑db option.

The ‑strand option is required for nucleotide databases.

Nucleotide, protein and translated searches are supported.

See also:
  Standard output file options
Accept options
  Weak hits
  Termination options
  Alignment parameters
  Alignment heuristics


usearch -search_local query.fasta -db db.fasta -evalue 10 -alnout results.aln