phmmer(1) HMMER Manual phmmer(1)NAMEphmmer - search protein sequence(s) against a protein sequence database
SYNOPSISphmmer [options] <seqfile> <seqdb>
DESCRIPTIONphmmer 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.
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.
-A <f> Save a multiple alignment of all significant hits (those satis‐
fying 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 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 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.
--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 avail‐
able as a file). The format of a substitution matrix <mxfile>
is the standard format accepted by BLAST, FASTA, and other
sequence analysis software.
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 addi‐
tional false positive domains in the smaller search space of
those comparisons that already satisfied the per-target 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 CONTROLLING INCLUSION THRESHOLDS
Inclusion thresholds are stricter than reporting thresholds. They con‐
trol 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 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. 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 fil‐
ter is the fastest and most approximate; the last is the full Forward
scoring algorithm, slowest but most accurate. There is also a bias fil‐
ter 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 con‐
sideration; changing filter thresholds does not alter bit scores, E-
values, or alignments, all of which are determined solely in postpro‐
cessing.
--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 For‐
ward 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.
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 loca‐
tion 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 loca‐
tion 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 loca‐
tion 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 esti‐
mates 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 ran‐
dom number generator is seeded arbitrarily, and stochastic simu‐
lations 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 for‐
mats 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 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 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 run‐
ning 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
(@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@ phmmer(1)
