hmmscan(1) HMMER Manual hmmscan(1)NAMEhmmscan - search sequence(s) against a profile database
SYNOPSIShmmscan [options] <hmmdb> <seqfile>
DESCRIPTIONhmmscan is used to search sequences against collections of profiles.
For each sequence in <seqfile>, use that query sequence to search the
target database of profiles in <hmmdb>, and output ranked lists of the
profiles with the most significant matches to the sequence.
The <seqfile> may contain more than one query sequence. It can be in
FASTA format, or several other common sequence file formats (genbank,
embl, and uniprot, among others), or in alignment file formats (stock‐
holm, aligned fasta, and others). See the --qformat option for a com‐
plete list.
The <hmmdb> needs to be press'ed using hmmpress before it can be
searched with hmmscan. This creates four binary files, suffixed
.h3{fimp}.
The output format is designed to be human-readable, but is often so
voluminous that reading it is impractical, and parsing it is a pain.
The --tblout and --domtblout options save output in simple tabular for‐
mats that are concise and easier to parse. The -o option allows redi‐
recting the main output, including throwing it away in /dev/null.
OPTIONS-h Help; print a brief reminder of command line usage and all
available options.
OPTIONS FOR CONTROLLING OUTPUT-o <f> Direct the main human-readable output to a file <f> instead of
the default stdout.
--tblout <f>
Save a simple tabular (space-delimited) file summarizing the
per-target output, with one data line per homologous target
model found.
--domtblout <f>
Save a simple tabular (space-delimited) file summarizing the
per-domain output, with one data line per homologous domain
detected in a query sequence for each homologous model.
--acc Use accessions instead of names in the main output, where avail‐
able for profiles and/or sequences.
--noali
Omit the alignment section from the main output. This can
greatly reduce the output volume.
--notextw
Unlimit the length of each line in the main output. The default
is a limit of 120 characters per line, which helps in displaying
the output cleanly on terminals and in editors, but can truncate
target profile description lines.
--textw <n>
Set the main output's line length limit to <n> characters per
line. The default is 120.
OPTIONS FOR REPORTING THRESHOLDS
Reporting thresholds control which hits are reported in output files
(the main output, --tblout, and --domtblout).
-E <x> In the per-target output, report target profiles with an E-value
of <= <x>. The default is 10.0, meaning that on average, about
10 false positives will be reported per query, so you can see
the top of the noise and decide for yourself if it's really
noise.
-T <x> Instead of thresholding per-profile output on E-value, instead
report target profiles with a bit score of >= <x>.
--domE <x>
In the per-domain output, for target profiles that have already
satisfied the per-profile reporting threshold, report individual
domains with a conditional E-value of <= <x>. The default is
10.0. A conditional E-value means the expected number of addi‐
tional false positive domains in the smaller search space of
those comparisons that already satisfied the per-profile report‐
ing threshold (and thus must have at least one homologous domain
already).
--domT <x>
Instead of thresholding per-domain output on E-value, instead
report domains with a bit score of >= <x>.
OPTIONS FOR INCLUSION THRESHOLDS
Inclusion thresholds are stricter than reporting thresholds. Inclusion
thresholds control which hits are considered to be reliable enough to
be included in an output alignment or a subsequent search round. In
hmmscan, which does not have any alignment output (like hmmsearch or
phmmer) nor any iterative search steps (like jackhmmer), inclusion
thresholds have little effect. They only affect what domains get marked
as significant (!) or questionable (?) in domain output.
--incE <x>
Use an E-value of <= <x> as the per-target inclusion threshold.
The default is 0.01, meaning that on average, about 1 false pos‐
itive would be expected in every 100 searches with different
query sequences.
--incT <x>
Instead of using E-values for setting the inclusion threshold,
instead use a bit score of >= <x> as the per-target inclusion
threshold. It would be unusual to use bit score thresholds with
hmmscan, because you don't expect a single score threshold to
work for different profiles; different profiles have slightly
different expected score distributions.
--incdomE <x>
Use a conditional E-value of <= <x> as the per-domain inclusion
threshold, in targets that have already satisfied the overall
per-target inclusion threshold. The default is 0.01.
--incdomT <x>
Instead of using E-values, instead use a bit score of >= <x> as
the per-domain inclusion threshold. As with --incT above, it
would be unusual to use a single bit score threshold in hmmscan.
OPTIONS FOR MODEL-SPECIFIC SCORE THRESHOLDING
Curated profile databases may define specific bit score thresholds for
each profile, superseding any thresholding based on statistical signif‐
icance alone.
To use these options, the profile must contain the appropriate (GA, TC,
and/or NC) optional score threshold annotation; this is picked up by
hmmbuild from Stockholm format alignment files. Each thresholding
option has two scores: the per-sequence threshold <x1> and the per-
domain threshold <x2> These act as if -T<x1> --incT<x1> --domT<x2>
--incdomT<x2> has been applied specifically using each model's curated
thresholds.
--cut_ga
Use the GA (gathering) bit scores in the model to set per-
sequence (GA1) and per-domain (GA2) reporting and inclusion
thresholds. GA thresholds are generally considered to be the
reliable curated thresholds defining family membership; for
example, in Pfam, these thresholds define what gets included in
Pfam Full alignments based on searches with Pfam Seed models.
--cut_nc
Use the NC (noise cutoff) bit score thresholds in the model to
set per-sequence (NC1) and per-domain (NC2) reporting and inclu‐
sion thresholds. NC thresholds are generally considered to be
the score of the highest-scoring known false positive.
--cut_tc
Use the NC (trusted cutoff) bit score thresholds in the model to
set per-sequence (TC1) and per-domain (TC2) reporting and inclu‐
sion thresholds. TC thresholds are generally considered to be
the score of the lowest-scoring known true positive that is
above all known false positives.
CONTROL OF THE ACCELERATION PIPELINE
HMMER3 searches are accelerated in a three-step filter pipeline: the
MSV filter, the Viterbi filter, and the Forward filter. The first fil‐
ter is the fastest and most approximate; the last is the full Forward
scoring algorithm. There is also a bias filter step between MSV and
Viterbi. Targets that pass all the steps in the acceleration pipeline
are then subjected to postprocessing -- domain identification and scor‐
ing using the Forward/Backward algorithm.
Changing filter thresholds only removes or includes targets from con‐
sideration; changing filter thresholds does not alter bit scores, E-
values, or alignments, all of which are determined solely in postpro‐
cessing.
--max Turn off all filters, including the bias filter, and run full
Forward/Backward postprocessing on every target. This increases
sensitivity somewhat, at a large cost in speed.
--F1 <x>
Set the P-value threshold for the MSV filter step. The default
is 0.02, meaning that roughly 2% of the highest scoring nonho‐
mologous targets are expected to pass the filter.
--F2 <x>
Set the P-value threshold for the Viterbi filter step. The
default is 0.001.
--F3 <x>
Set the P-value threshold for the Forward filter step. The
default is 1e-5.
--nobias
Turn off the bias filter. This increases sensitivity somewhat,
but can come at a high cost in speed, especially if the query
has biased residue composition (such as a repetitive sequence
region, or if it is a membrane protein with large regions of
hydrophobicity). Without the bias filter, too many sequences may
pass the filter with biased queries, leading to slower than
expected performance as the computationally intensive For‐
ward/Backward algorithms shoulder an abnormally heavy load.
OTHER OPTIONS--nonull2
Turn off the null2 score corrections for biased composition.
-Z <x> Assert that the total number of targets in your searches is <x>,
for the purposes of per-sequence E-value calculations, rather
than the actual number of targets seen.
--domZ <x>
Assert that the total number of targets in your searches is <x>,
for the purposes of per-domain conditional E-value calculations,
rather than the number of targets that passed the reporting
thresholds.
--seed <n>
Set the random number seed to <n>. Some steps in postprocessing
require Monte Carlo simulation. The default is to use a fixed
seed (42), so that results are exactly reproducible. Any other
positive integer will give different (but also reproducible)
results. A choice of 0 uses an arbitrarily chosen seed.
--qformat <s>
Assert that the query sequence file is in format <s>. Accepted
formats include fasta, embl, genbank, ddbj, uniprot, stockholm,
pfam, a2m, and afa.
--cpu <n>
Set the number of parallel worker threads to <n>. By default,
HMMER sets this to the number of CPU cores it detects in your
machine - that is, it tries to maximize the use of your avail‐
able processor cores. Setting <n> higher than the number of
available cores is of little if any value, but you may want to
set it to something less. You can also control this number by
setting an environment variable, HMMER_NCPU.
This option is only available if HMMER was compiled with POSIX
threads support. This is the default, but it may have been
turned off for your site or machine for some reason.
--stall
For debugging the MPI master/worker version: pause after start,
to enable the developer to attach debuggers to the running mas‐
ter and worker(s) processes. Send SIGCONT signal to release the
pause. (Under gdb: (gdb) signal SIGCONT)
(Only available if optional MPI support was enabled at compile-
time.)
--mpi Run in MPI master/worker mode, using mpirun.
(Only available if optional MPI support was enabled at compile-
time.)
SEE ALSO
See hmmer(1) for a master man page with a list of all the individual
man pages for programs in the HMMER package.
For complete documentation, see the user guide that came with your
HMMER distribution (Userguide.pdf); or see the HMMER web page
(@HMMER_URL@).
COPYRIGHT
@HMMER_COPYRIGHT@
@HMMER_LICENSE@
For additional information on copyright and licensing, see the file
called COPYRIGHT in your HMMER source distribution, or see the HMMER
web page (@HMMER_URL@).
AUTHOR
Eddy/Rivas Laboratory
Janelia Farm Research Campus
19700 Helix Drive
Ashburn VA 20147 USA
http://eddylab.org
HMMER @HMMER_VERSION@ @HMMER_DATE@ hmmscan(1)
