NAME¶
hmmscan - search protein sequence(s) against a protein profile database
SYNOPSIS¶
hmmscan [options] <hmmdb> <seqfile>
DESCRIPTION¶
hmmscan is used to search protein sequences against collections of
protein 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 (stockholm, aligned
fasta, and others). See the
--qformat option for a complete 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 query
<seqfile> may be '-' (a dash character), in which case
the query sequences are read from a <stdin> pipe instead of from a file.
The
<hmmdb> cannot be read from a <stdin> stream, because
it needs to have those four auxiliary binary files generated by
hmmpress.
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 formats that are
concise and easier to parse. The
-o option allows redirecting 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.
- --pfamtblout <f>
- Save an especially succinct tabular (space-delimited) file summarizing the
per-target output, with one data line per homologous target model found.
- --acc
- Use accessions instead of names in the main output, where available 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 additional false positive
domains in the smaller search space of those comparisons that already
satisfied the per-profile reporting 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
positive 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 significance 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 inclusion
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 inclusion
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 filter 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 scoring using the Forward/Backward algorithm.
Changing filter thresholds only removes or includes targets from consideration;
changing filter thresholds does not alter bit scores, E-values, or alignments,
all of which are determined solely in postprocessing.
- --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 nonhomologous 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
Forward/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 available 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 master 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 ().
COPYRIGHT¶
Copyright (C) 2013 Howard Hughes Medical Institute.
Freely distributed under the GNU General Public License (GPLv3).
For additional information on copyright and licensing, see the file called
COPYRIGHT in your HMMER source distribution, or see the HMMER web page ().
AUTHOR¶
Eddy/Rivas Laboratory
Janelia Farm Research Campus
19700 Helix Drive
Ashburn VA 20147 USA
http://eddylab.org