Commands > Search
Search for matches of protein sequences to a database containing short amino
acid sequences (peptides)..
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 short
peptides. The name of the command (search_peptidedb)
is intended to remind you of this.
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
are supported for nucleotide queries.
Standard output files
usearch -search_peptides proteomes.fa -db peptides.fa \
-userfields out.txt -userfields