NAME¶
phmmer - search protein sequence(s) against a protein sequence database
SYNOPSIS¶
phmmer [options] <seqfile> <seqdb>
DESCRIPTION¶
phmmer is used to search one or more query protein sequences against a
protein sequence database. For each query sequence in
<seqfile>,
use that sequence to search the target database of sequences in
<seqdb>, and output ranked lists of the sequences with the most
significant matches to the query.
Either the query
<seqfile> or the target
<seqdb> may
be '-' (a dash character), in which case the query sequences or target
database input will be read from a <stdin> pipe instead of from a file.
Only one input source can come through <stdin>, not both. An exception
is that if the
<seqfile> contains more than one query sequence,
then
<seqdb> cannot come from <stdin>, because we can't
rewind the streaming target database to search it with another query.
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.
- -A <f>
- Save a multiple alignment of all significant hits (those satisfying
inclusion thresholds) to the file <f> in Stockholm format.
- --tblout <f>
- Save a simple tabular (space-delimited) file summarizing the per-target
output, with one data line per homologous target sequence 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 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 CONTROLLING SCORING SYSTEM¶
The probability model in
phmmer is constructed by inferring residue
probabilities from a standard 20x20 substitution score matrix, plus two
additional parameters for position-independent gap open and gap extend
probabilities.
- --popen <x>
- Set the gap open probability for a single sequence query model to
<x>. The default is 0.02. <x> must be >= 0
and < 0.5.
- --pextend <x>
- Set the gap extend probability for a single sequence query model to
<x>. The default is 0.4. <x> must be >= 0 and
< 1.0.
- --mx <s>
- Obtain residue alignment probabilities from the built-in substitution
matrix named <s>. Several standard matrices are built-in, and
do not need to be read from files. The matrix name <s> can be
PAM30, PAM70, PAM120, PAM240, BLOSUM45, BLOSUM50, BLOSUM62, BLOSUM80, or
BLOSUM90. Only one of the --mx and --mxfile options may be
used.
- --mxfile <mxfile>
- Obtain residue alignment probabilities from the substitution matrix in
file <mxfile>. The default score matrix is BLOSUM62 (this
matrix is internal to HMMER and does not have to be available as a file).
The format of a substitution matrix <mxfile> is the standard
format accepted by BLAST, FASTA, and other sequence analysis software.
Only one of the --mx and --mxfile options may be used.
OPTIONS CONTROLLING REPORTING THRESHOLDS¶
Reporting thresholds control which hits are reported in output files (the main
output,
--tblout, and
--domtblout). Sequence hits and domain
hits are ranked by statistical significance (E-value) and output is generated
in two sections called per-target and per-domain output. In per-target output,
by default, all sequence hits with an E-value <= 10 are reported. In the
per-domain output, for each target that has passed per-target reporting
thresholds, all domains satisfying per-domain reporting thresholds are
reported. By default, these are domains with conditional E-values of <= 10.
The following options allow you to change the default E-value reporting
thresholds, or to use bit score thresholds instead.
- -E <x>
- In the per-target output, report target sequences 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 sequences with a bit score of >= <x>.
- --domE <x>
- In the per-domain output, for target sequences 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-target 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 CONTROLLING INCLUSION THRESHOLDS¶
Inclusion thresholds are stricter than reporting thresholds. They control which
hits are included in any output multiple alignment (the
-A option) and
which domains are marked as significant ("!") as opposed to
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. By default this option is unset.
- --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, use a bit score of >= <x> as
the per-domain inclusion threshold. By default this option is unset.
OPTIONS CONTROLLING 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, slowest
but most accurate. 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.
Essentially the only free parameters that control HMMER's heuristic filters are
the P-value thresholds controlling the expected fraction of nonhomologous
sequences that pass the filters. Setting the default thresholds higher will
pass a higher proportion of nonhomologous sequence, increasing sensitivity at
the expense of speed; conversely, setting lower P-value thresholds will pass a
smaller proportion, decreasing sensitivity and increasing speed. Setting a
filter's P-value threshold to 1.0 means it will passing all sequences, and
effectively disables the filter.
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
- Maximum sensitivity. Turn off all filters, including the bias filter, and
run full Forward/Backward postprocessing on every target. This increases
sensitivity slightly, at a large cost in speed.
- --F1 <x>
- First filter threshold; 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>
- Second filter threshold; set the P-value threshold for the Viterbi filter
step. The default is 0.001.
- --F3 <x>
- Third filter threshold; 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.
OPTIONS CONTROLLING E-VALUE CALIBRATION¶
Estimating the location parameters for the expected score distributions for MSV
filter scores, Viterbi filter scores, and Forward scores requires three short
random sequence simulations.
- --EmL <n>
- Sets the sequence length in simulation that estimates the location
parameter mu for MSV filter E-values. Default is 200.
- --EmN <n>
- Sets the number of sequences in simulation that estimates the location
parameter mu for MSV filter E-values. Default is 200.
- --EvL <n>
- Sets the sequence length in simulation that estimates the location
parameter mu for Viterbi filter E-values. Default is 200.
- --EvN <n>
- Sets the number of sequences in simulation that estimates the location
parameter mu for Viterbi filter E-values. Default is 200.
- --EfL <n>
- Sets the sequence length in simulation that estimates the location
parameter tau for Forward E-values. Default is 100.
- --EfN <n>
- Sets the number of sequences in simulation that estimates the location
parameter tau for Forward E-values. Default is 200.
- --Eft <x>
- Sets the tail mass fraction to fit in the simulation that estimates the
location parameter tau for Forward evalues. Default is 0.04.
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>
- Seed the random number generator with <n>, an integer >=
0. If <n> is >0, any stochastic simulations will be
reproducible; the same command will give the same results. If
<n> is 0, the random number generator is seeded arbitrarily,
and stochastic simulations will vary from run to run of the same command.
The default seed is 42.
- --qformat <s>
- Declare that the input <seqfile> is in format
<s>. Accepted formats include fasta, embl,
genbank, ddbj, uniprot, stockholm,
pfam, a2m, and afa. The default is to autodetect the
format of the file.
- --tformat <s>
- Declare that the input <seqdb> is in format <s>.
Accepted formats include fasta, embl, genbank,
ddbj, uniprot, stockholm, pfam, a2m,
and afa. The default is to autodetect the format of the file.
- --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 at
compile-time 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