| 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. USEARCH 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. The
usearch_local command is rarely, if ever, used in practice. It is
provided for completeness because it was easy to implement in the code, but I
don't know of a single case where I would recommend it over ublast or
usearch_global. If you find it useful, please let me know. 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: Examples usearch -usearch_local query.fasta -db
proteins.udb -id 0.8 -alnout results.aln |