Comprehensive database search. All database sequences are aligned to the query, no index is used. Alignments are local. Much slower than usearch_local or ublast for large datasets; mostly useful for ad hoc queries on small datasets. A hit will be found only if there is at least one exact matching word of length -hspw, which defaults to 3 for proteins and 5 for nucleotides, or the -fulldp option is specified (see alignment heuristics).
An E-value threshold must be specified using the -evalue option.
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.
Standard output file options
usearch -search_local query.fasta -db db.fasta
-evalue 10 -alnout results.aln