USEARCH searches a database for the
top global hit, or top few hits. This is distinctly different from
traditional search algorithms such as BLAST, which use local alignments and
report all hits at a given E-value threshold.
The advantages of the USEARCH algorithm include its ultra-high speed, which
can be orders of magnitude faster than BLAST, and reduced data output since in
most applications only the top hit or the top few hits are relevant. Also, in
some applications, e,g, taxonomy assignment, global alignments give better
biological predictions as local alignments may give short hits with misleadingly
The USEARCH algorithm is
implemented in the usearch_global command.
A local alignment variant is also provided (usearch_local),
though this is rarely used in practice. USEARCH is not effective on very large
databases, say much greater than 1M sequences or 1Gb as a FASTA file. For huge
databases, UBLAST is recommended even if global hits are required.
For both USEARCH and UBLAST commands,
accept parameters give a rich set of options for filtering hits.