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
An identity threshold must be specified using
the ‑id option. An E-value threshold may
also be specified.
file must be specified using the ‑db option.
option is required for nucleotide databases.
Nucleotide, protein and translated searches are
See search flowchart
for overview of searching in USEARCH commands.
Standard output file
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