Commands > Search
Search for matches of nucleotide sequences to a database containing short
nucleotide sequences (oligonucleotides). The most common use for this command is
searching for matches to primers or probes in genome sequences or gene
Wildcard letters indicating degenerate
positions in the primer are supported. See IUPAC
codes for details.
The algorithm uses a fast and exact method; there are
no heuristics, so all matches meeting the accept criteria are guaranteed to be
found. Alignments are global; all letters of the database sequence must be
aligned to a letter in the query sequence. Gaps are not permitted, except for
terminal gaps in the query sequence.
Note that it is the longer sequence (genome,
chromosome, gene etc.) that is the query; the
database contains the oligos. The
name of the command (search_oligodb)
is intended to remind you of this, just in case you're used to doing it the
other way around, as with some other local aligners like BLAST.
are supported. By default, termination is disabled, equivalent to -maxaccepts 0
-maxrejects 0. In other words, by default the entire database is searched.
Accept options are
supported. By default, -maxdiffs 2 is assumed and other accept criteria are not
The query file may be in
FASTA or FASTQ format.
file must be specified using the ‑db option and must be in
option is required for nucleotide databases.
Standard output files
usearch -search_oligodb human_genome.fa -db probes.fa
-strand both \
-userout out.txt -userfields