nhmmer - Online in the Cloud

PROGRAM:

NAME

nhmmer - search DNA/RNA queries against a DNA/RNA sequence database

SYNOPSIS

nhmmer [options] <queryfile> <seqdb>

DESCRIPTION

nhmmer is used to search one or more nucleotide queries against a nucleotide sequence
database. For each query in <queryfile>, use that query to search the target database of
sequences in <seqdb>, and output a ranked list of the hits with the most significant
matches to the query. A query may be either a profile model built using hmmbuild, a
sequence alignment, or a single sequence. Sequence based queries can be in a number of
formats (see --qformat), and can typically be autodetected. Note that only Stockholm
format supports queries made up of more than one sequence alignment.

Either the query <queryfile> or the target <seqdb> may be '-' (a dash character), in which
case the query file 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. If the query is
sequence-based and passed via <stdin>, the --qformat flag must be used. If the
<queryfile> contains more than one query, then <seqdb> cannot come from <stdin>, because
we can't rewind the streaming target database to search it with another profile.

If the query is sequence-based, and not from <stdin>, a new file containing the HMM(s)
built from the input(s) in <queryfile> may optionally be produced, with the filename set
using the --hmmout flag.

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 option saves output in a
simple tabular format that is 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>.

--tblout <f>
Save a simple tabular (space-delimited) file summarizing the per-target output,
with one data line per homologous target sequence found.

--dfamtblout <f>
Save a tabular (space-delimited) file summarizing the per-hit output, similar to
--tblout but more succinct.

--aliscoresout <f>
Save to file a list of per-position scores for each hit. This is useful, for
example, in identifying regions of high score density for use in resolving
overlapping hits from different models.

--hmmout <f>
If <queryfile> is sequence-based, write the internally-computed HMM(s) to <f>.

--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 REPORTING THRESHOLDS

Reporting thresholds control which hits are reported in output files (the main output,
--tblout, and --dfamtblout). Hits are ranked by statistical significance (E-value).

-E <x> 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 output on E-value, instead report target sequences 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, or marked as significant ("!") as opposed to questionable ("?")
in hit output.

--incE <x>
Use an E-value of <= <x> as the 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, use a bit score of
>= <x> as the inclusion threshold. By default this option is unset.

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. For a nucleotide model, each thresholding option has a single per-hit
threshold <x> This acts as if -T<x> --incT<x> has been applied specifically using each
model's curated thresholds.

--cut_ga
Use the GA (gathering) bit score threshold in the model to set per-hit reporting
and inclusion thresholds. GA thresholds are generally considered to be the reliable
curated thresholds defining family membership; for example, in Dfam, these
thresholds are applied when annotating a genome with a model of a family known to
be found in that organism. They may allow for minimal expected false discovery
rate.

--cut_nc
Use the NC (noise cutoff) bit score threshold in the model to set per-hit reporting
and inclusion thresholds. NC thresholds are less stringent than GA; in the context
of Pfam, they are generally used to store the score of the highest-scoring known
false positive.

--cut_tc
Use the NC (trusted cutoff) bit score threshold in the model to set per-hit
reporting and inclusion thresholds. TC thresholds are more stringent than GA, and
are generally considered to be the score of the lowest-scoring known true positive
that is above all known false positives; for example, in Dfam, these thresholds are
applied when annotating a genome with a model of a family not known to be found in
that organism.

OPTIONS CONTROLLING THE ACCELERATION PIPELINE

HMMER3 searches are accelerated in a three-step filter pipeline: the scanning-SSV 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 SSV 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 (nearly) all filters, including the bias filter, and run full
Forward/Backward postprocessing on most of the target sequence. In contrast to
phmmer and hmmsearch, where this flag really does turn off the filters entirely,
the --max flag in nhmmer sets the scanning-SSV filter threshold to 0.4, not 1.0.
Use of this flag increases sensitivity somewhat, at a large cost in speed.

--F1 <x>
Set the P-value threshold for the SSV 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.

OPTIONS FOR SPECIFYING THE ALPHABET

The alphabet type of the target database (DNA or RNA) is autodetected by default, by
looking at the composition of the <seqdb>. Autodetection is normally quite reliable, but
occasionally alphabet type may be ambiguous and autodetection can fail (for instance, when
the first sequence starts with a run of ambiguous characters). To avoid this, or to
increase robustness in automated analysis pipelines, you may specify the alphabet type of
<seqdb> with these options.

--dna Specify that all sequences in <seqdb> are DNAs.

--rna Specify that all sequences in <seqdb> are RNAs.

OPTIONS CONTROLLING SEED SEARCH HEURISTIC

When searching with nhmmer, one may optionally precompute a binary version of the target
database, using makehmmerdb, then search against that database. Using default settings,
this yields a roughly 10-fold acceleration with small loss of sensitivity on benchmarks.
This is achieved using a heuristic method that searches for seeds (ungapped alignments)
around which full processing is done. This is essentially a replacement to the SSV stage.
(This method has been extensively tested, but should still be treated as somewhat
experimental.) The following options only impact nhmmer if the value of --tformat is
hmmerdb.

Changing parameters for this seed-finding step will impact both speed and sensitivity -
typically faster search leads to lower sensitivity.

--seed_max_depth <n>
The seed step requires that a seed reach a specified bit score in length no longer
than <n>. By default, this value is 15. Longer seeds allow a greater chance of
meeting the bit score threshold, leading to diminished filtering (greater
sensitivity, slower run time).

--seed_sc_thresh <x>
The seed must reach score <x> (in bits). The default is 15.0 bits. A higher
threshold increases filtering stringency, leading to faster run times and lower
sensitivity.

--seed_sc_density <x>
Either all prefixes or all suffixes of a seed must have bit density (bits per
aligned position) of at least <x>. The default is 0.8 bits/position. An increase
in the density requirement leads to increased filtering stringency, thus faster run
times and lower sensitivity.

--seed_drop_max_len <n>
A seed may not have a run of length <n> in which the score drops by --seed_drop_lim
or more. Basically, this prunes seeds that go through long slightly-negative seed
extensions. The default is 4. Increasing the limit causes (slightly) diminished
filtering efficiency, thus slower run times and higher sensitivity. (minor tuning
option)

--seed_drop_lim <x>
In a seed, there may be no run of length --seed_drop_max_len in which the score
drops by --seed_drop_lim. The default is 0.3 bits. Larger numbers mean less
filtering. (minor tuning option)

--seed_req_pos <n>
A seed must contain a run of at least <n> positive-scoring matches. The default is
5. Larger values mean increased filtering. (minor tuning option)

--seed_ssv_length <n>
After finding a short seed, an ungapped alignment is extended in both directions in
an attempt to meet the --F1 score threshold. The window through which this ungapped
alignment extends is length <n>. The default is 70. Decreasing this value
slightly reduces run time, at a small risk of reduced sensitivity. (minor tuning
option)

OTHER OPTIONS

--tformat <s>
Assert that the target sequence database file is in format <s>. Accepted formats
include fasta, embl, genbank, ddbj, uniprot, stockholm, pfam, a2m, afa, and
hmmerfm. The default is to autodetect the format of the file. The format hmmerfm
indicates that the database file is a binary file produced using makehmmerdb (this
format is not currently autodetected).

--qformat <s>
Declare that the input <queryfile> is in format <s>. This is used when the query
is sequence-based, rather than made up of profile model(s). Currently the accepted
multiple alignment sequence file formats include Stockholm, Aligned FASTA, Clustal,
NCBI PSI-BLAST, PHYLIP, Selex, and UCSC SAM A2M. Default is to autodetect the
format of the file.

--nonull2
Turn off the null2 score corrections for biased composition.

-Z <x> For the purposes of per-hit E-value calculations, Assert that the total size of the
target database is <x> million nucleotides, rather than the actual number of
targets seen.

--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 a randomly chosen seed.

--w_beta <x>
Window length tail mass. The upper bound, W, on the length at which nhmmer expects
to find an instance of the model is set such that the fraction of all sequences
generated by the model with length >= W is less than <x>. The default is 1e-7.
This flag may be used to override the value of W established for the model by
hmmbuild, or when the query is sequence-based.

--w_length <n>
Override the model instance length upper bound, W, which is otherwise controlled by
--w_beta. It should be larger than the model length. The value of W is used deep
in the acceleration pipeline, and modest changes are not expected to impact results
(though larger values of W do lead to longer run time). This flag may be used to
override the value of W established for the model by hmmbuild, or when the query is
sequence-based.

--toponly
Only search the top strand. By default both the query sequence and its reverse-
complement are searched.

--bottomonly
Only search the bottom (reverse-complement) strand. By default both the query
sequence and its reverse-complement are searched.

--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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