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PROGRAM:

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 0.0 means that every alignment column will
be assigned as consensus, which may be useful in some cases. Setting it to 1.0
means that only columns that include 0 gaps (internal insertions/deletions) will be
assigned as consensus.

--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.)

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