NAME¶
jackhmmer - iteratively search sequence(s) against a protein database
SYNOPSIS¶
jackhmmer [options] <seqfile> <seqdb>
DESCRIPTION¶
jackhmmer iteratively searches each query sequence in
<seqfile> against the target sequence(s) in
<seqdb>.
The first iteration is identical to a
phmmer search. For the next
iteration, a multiple alignment of the query together with all target
sequences satisfying
inclusion thresholds is assembled, a profile is
constructed from this alignment (identical to using
hmmbuild on the
alignment), and profile search of the
<seqdb> is done (identical
to an
hmmsearch with the profile).
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
<seqdb> cannot be read from a <stdin> stream, because
jackhmmer needs to do multiple passes over the database.
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.
- -N <n>
- Set the maximum number of iterations to <n>. The default is
5. If N=1, the result is equivalent to a phmmer search.
OPTIONS CONTROLLING OUTPUT¶
By default, output for each iteration appears on stdout in a somewhat human
readable, somewhat parseable format. These options allow redirecting that
output or saving additional kinds of output to files, including checkpoint
files for each iteration.
- -o <f>
- Direct the human-readable output to a file <f>.
- -A <f>
- After the final iteration, save an annotated multiple alignment of all
hits satisfying inclusion thresholds (also including the original query)
to <f> in Stockholm format.
- --tblout <f>
- After the final iteration, save a tabular summary of top sequence hits to
<f> in a readily parseable, columnar, whitespace-delimited
format.
- --domtblout <f>
- After the final iteration, save a tabular summary of top domain hits to
<f> in a readily parseable, columnar, whitespace-delimited
format.
- --chkhmm <prefix>
- At the start of each iteration, checkpoint the query HMM, saving it to a
file named <prefix>-<n>.hmm where <n> is
the iteration number (from 1..N).
- --chkali <prefix>
- At the end of each iteration, checkpoint an alignment of all domains
satisfying inclusion thresholds (e.g. what will become the query HMM for
the next iteration), saving it to a file named <checkpoint file
prefix>-<n>.sto in Stockholm format, where <n>
is the iteration number (from 1..N).
- --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 SINGLE SEQUENCE SCORING (FIRST ITERATION)¶
By default, the first iteration uses a search model constructed from a single
query sequence. This model is constructed using a standard 20x20 substitution
matrix for residue probabilities, and two additional parameters for
position-independent gap open and gap extend probabilities. These options
allow the default single-sequence scoring parameters to be changed.
- --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.
OPTIONS CONTROLLING REPORTING THRESHOLDS¶
Reporting thresholds control which hits are reported in output files (the main
output,
--tblout, and
--domtblout). In each iteration, 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>
- Report sequences with E-values <= <x> in per-sequence
output. The default is 10.0.
- -T <x>
- Use a bit score threshold for per-sequence output instead of an E-value
threshold (any setting of -E is ignored). Report sequences with a
bit score of >= <x>. By default this option is unset.
- -Z <x>
- Declare the total size of the database to be <x> sequences,
for purposes of E-value calculation. Normally E-values are calculated
relative to the size of the database you actually searched (e.g. the
number of sequences in target_seqdb). In some cases (for instance,
if you've split your target sequence database into multiple files for
parallelization of your search), you may know better what the actual size
of your search space is.
- --domE <x>
- Report domains with conditional E-values <= <x> in
per-domain output, in addition to the top-scoring domain per significant
sequence hit. The default is 10.0.
- --domT <x>
- Use a bit score threshold for per-domain output instead of an E-value
threshold (any setting of --domT is ignored). Report domains with a
bit score of >= <x> in per-domain output, in addition to
the top-scoring domain per significant sequence hit. By default this
option is unset.
- --domZ <x>
- Declare the number of significant sequences to be <x>
sequences, for purposes of conditional E-value calculation for additional
domain significance. Normally conditional E-values are calculated relative
to the number of sequences passing per-sequence reporting threshold.
OPTIONS CONTROLLING INCLUSION THRESHOLDS¶
Inclusion thresholds control which hits are included in the multiple alignment
and profile constructed for the next search iteration. By default, a sequence
must have a per-sequence E-value of <= 0.001 (see
-E option) to be
included, and any additional domains in it besides the top-scoring one must
have a conditional E-value of <= 0.001 (see
--domE option). The
difference between reporting thresholds and inclusion thresholds is that
inclusion thresholds control which hits actually get used in the next
iteration (or the final output multiple alignment if the
-A option is
used), whereas reporting thresholds control what you see in output. Reporting
thresholds are generally more loose so you can see borderline hits in the top
of the noise that might be of interest.
- --incE <x>
- Include sequences with E-values <= <x> in subsequent
iteration or final alignment output by -A. The default is 0.001.
- --incT <x>
- Use a bit score threshold for per-sequence inclusion instead of an E-value
threshold (any setting of --incE is ignored). Include sequences
with a bit score of >= <x>. By default this option is
unset.
- --incdomE <x>
- Include domains with conditional E-values <= <x> in
subsequent iteration or final alignment output by -A, in addition
to the top-scoring domain per significant sequence hit. The default is
0.001.
- --incdomT <x>
- Use a bit score threshold for per-domain inclusion instead of an E-value
threshold (any setting of --incT is ignored). Include domains with
a bit score of >= <x>. By default this option is unset.
OPTIONS CONTROLLING ACCELERATION HEURISTICS¶
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 PROFILE CONSTRUCTION (LATER ITERATIONS)¶
These options control how consensus columns are defined in multiple alignments
when building profiles. By default,
jackhmmer always includes your
original query sequence in the alignment result at every iteration, and
consensus positions are defined by that query sequence: that is, a default
jackhmmer profile is always the same length as your original query, at
every iteration.
- --fast
- Define consensus columns as those that have a fraction >=
symfrac of residues as opposed to gaps. (See below for the
--symfrac option.) Although this is the default profile
construction option elsewhere (in hmmbuild, in particular), it may
have undesirable effects in jackhmmer, because a profile could
iteratively walk in sequence space away from your original query, leaving
few or no consensus columns corresponding to its residues.
- --hand
- Define consensus columns in next profile using reference annotation to the
multiple alignment. jackhmmer propagates reference annotation from
the previous profile to the multiple alignment, and thence to the next
profile. This is the default.
- --symfrac <x>
- Define the residue fraction threshold necessary to define a consensus
column when using the --fast option. The default is 0.5. The symbol
fraction in each column is calculated after taking relative sequence
weighting into account, and ignoring gap characters corresponding to ends
of sequence fragments (as opposed to internal insertions/deletions).
Setting this to 1.0 means that every alignment column will be assigned as
consensus, which may be useful in some cases. Setting it to 0.0 is a bad
idea, because no columns will be assigned as consensus, and you'll get a
model of zero length.
- --fragthresh <x>
- We only want to count terminal gaps as deletions if the aligned sequence
is known to be full-length, not if it is a fragment (for instance, because
only part of it was sequenced). HMMER uses a simple rule to infer
fragments: if the sequence length L is less than or equal to a fraction
<x> times the alignment length in columns, then the sequence
is handled as a fragment. The default is 0.5. Setting
--fragthresh0 will define no (nonempty) sequence as a
fragment; you might want to do this if you know you've got a carefully
curated alignment of full-length sequences. Setting
--fragthresh1 will define all sequences as fragments; you
might want to do this if you know your alignment is entirely composed of
fragments, such as translated short reads in metagenomic shotgun data.
OPTIONS CONTROLLING RELATIVE WEIGHTS¶
Whenever a profile is built from a multiple alignment, HMMER uses an ad hoc
sequence weighting algorithm to downweight closely related sequences and
upweight distantly related ones. This has the effect of making models less
biased by uneven phylogenetic representation. For example, two identical
sequences would typically each receive half the weight that one sequence would
(and this is why
jackhmmer isn't concerned about always including your
original query sequence in each iteration's alignment, even if it finds it
again in the database you're searching). These options control which algorithm
gets used.
- --wpb
- Use the Henikoff position-based sequence weighting scheme [Henikoff and
Henikoff, J. Mol. Biol. 243:574, 1994]. This is the default.
- --wgsc
- Use the Gerstein/Sonnhammer/Chothia weighting algorithm [Gerstein et al,
J. Mol. Biol. 235:1067, 1994].
- --wblosum
- Use the same clustering scheme that was used to weight data in calculating
BLOSUM subsitution matrices [Henikoff and Henikoff, Proc. Natl. Acad. Sci
89:10915, 1992]. Sequences are single-linkage clustered at an identity
threshold (default 0.62; see --wid) and within each cluster of c
sequences, each sequence gets relative weight 1/c.
- --wnone
- No relative weights. All sequences are assigned uniform weight.
- --wid <x>
- Sets the identity threshold used by single-linkage clustering when using
--wblosum. Invalid with any other weighting scheme. Default is
0.62.
OPTIONS CONTROLLING EFFECTIVE SEQUENCE NUMBER¶
After relative weights are determined, they are normalized to sum to a total
effective sequence number,
eff_nseq. This number may be the actual
number of sequences in the alignment, but it is almost always smaller than
that. The default entropy weighting method
(--eent) reduces the
effective sequence number to reduce the information content (relative entropy,
or average expected score on true homologs) per consensus position. The target
relative entropy is controlled by a two-parameter function, where the two
parameters are settable with
--ere and
--esigma.
- --eent
- Adjust effective sequence number to achieve a specific relative entropy
per position (see --ere). This is the default.
- --eclust
- Set effective sequence number to the number of single-linkage clusters at
a specific identity threshold (see --eid). This option is not
recommended; it's for experiments evaluating how much better --eent
is.
- --enone
- Turn off effective sequence number determination and just use the actual
number of sequences. One reason you might want to do this is to try to
maximize the relative entropy/position of your model, which may be useful
for short models.
- --eset <x>
- Explicitly set the effective sequence number for all models to
<x>.
- --ere <x>
- Set the minimum relative entropy/position target to <x>.
Requires --eent. Default depends on the sequence alphabet; for
protein sequences, it is 0.59 bits/position.
- --esigma <x>
- Sets the minimum relative entropy contributed by an entire model
alignment, over its whole length. This has the effect of making short
models have higher relative entropy per position than --ere alone
would give. The default is 45.0 bits.
- --eid <x>
- Sets the fractional pairwise identity cutoff used by single linkage
clustering with the --eclust option. The default is 0.62.
OPTIONS CONTROLLING PRIORS¶
In profile construction, by default, weighted counts are converted to mean
posterior probability parameter estimates using mixture Dirichlet priors.
Default mixture Dirichlet prior parameters for protein models and for nucleic
acid (RNA and DNA) models are built in. The following options allow you to
override the default priors.
--pnone Don't use any priors. Probability parameters will simply be the
observed frequencies, after relative sequence weighting.
--plaplace Use a Laplace +1 prior in place of the default mixture
Dirichlet prior.
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 query_seqfile is in format <s>.
Accepted sequence file formats include FASTA, EMBL, GenBank, DDBJ,
UniProt, Stockholm, and SELEX. Default is to autodetect the format of the
file.
- --tformat <s>
- Declare that the input target_seqdb is in format <s>.
Accepted sequence file formats include FASTA, EMBL, GenBank, DDBJ,
UniProt, Stockholm, and SELEX. 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