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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. 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.
 
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 also:
  Standard output file options
 
Accept options
  Weak hits
  Termination options
  Indexing options
  Multithreading
  Masking options
  Alignment parameters
  Alignment heuristics

Examples

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