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usearch_local command
Search for one (default) or a few high-identity hits to a database using the USEARCH algorithm. Alignments are local. To get more than one hit, increase -maxaccepts. The USEARCH algorithm is generally best suited for global alignments, but local searches may sometimes be appropriate and effective. This is the case when the local alignments cover a large enough fraction of both the query and target sequence that the common word count between the full-length sequences correlates with similarity in the region. Increasing ‑maxrejects may improve sensitivity when this assumption holds less well.

An identity threshold must be specified using the ‑id option. An E-value threshold may also be specified.

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 search flowchart for overview of searching in USEARCH commands.

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


usearch -usearch_local query.fasta -db proteins.udb -id 0.8 -alnout results.aln
usearch -usearch_local query.fasta -db ESTs.fasta -id 0.9  -evalue 1e-6 \
  -blast6out results.m8 -strand plus -maxaccepts 8 -maxrejects 256