Commands > Search
The search_exact command searches for exact, full-length
matches to a database sequence. The algorithm is faster than
usearch_global, uses less memory, and is
guaranteed to find all correct matches, i.e. there are no heuristics.
underlying algorithm is the same as for the
The query sequences may be in FASTA or FASTQ format.
The database file must be in FASTA format. Indexed (udb)
databases are not supported.
option is required for nucleotide databases. If -strand both is specified, then
reverse-complemented exact matches will also be reported.
Standard output file
options are supported. For example, the -notmatched
output file can be used to save query sequences that are not found in the
database and the -dbnotmatched option can be
used to save database sequences that are not present in the query set. This
enables incremental updating of dereplicated
usearch -search_exact seqs.fa -db
db.fa -blast6out matches.b6 -strand plus