search a DNA model or alignment against a DNA database (BLASTN-like)
macros.xml
'$output'
]]>
, use that query to search the
target database of sequences in , and output a ranked list of the hits
with the most significant matches to the query. A query may be either a profile
model built using hmmbuild, a sequence alignment, or a single sequence.
Sequence based queries can be in a number of formats (see --qformat), and can
typically be autodetected. Note that only Stockholm format supports the use of
multiple sequence-based queries.
@HELP_PRE_OTH@
@OFORMAT_WITH_OPTS_N_HELP@
@HSSI_HELP@
@THRESHOLDS_NODOM_HELP@
@CUT_HELP@
@ACCEL_HEUR_HELP@
@FORMAT_SELECTOR_HELP@
@ADV_OPTS_HELP@
@LENGTHS_HELP@
@SEED_HELP@
@ATTRIBUTION@
]]>