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 well.
Usually, ublast should be used instead of
An identity threshold must be specified using the -id option. An E-value threshold may also be specified.
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 -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 \
-userout hits.txt -userfield query+target+evalue+id