nhmmscan - search DNA sequence(s) against a DNA profile database
] hmmdb seqfile
is used to search nucleotide sequences against collections of
nucleotide profiles. For each sequence in seqfile
, use that query
sequence to search the target database of profiles in hmmdb
, and output
ranked lists of the profiles with the most significant matches to the
may contain more than one query sequence. It can be in FASTA
format, or several other common sequence file formats (genbank, embl, and
uniprot, among others), or in alignment file formats (stockholm, aligned
fasta, and others). See the --qformat
option for a complete list.
needs to be press'ed using hmmpress
before it can be
searched with nhmmscan
. This creates four binary files, suffixed
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 hmmdb
cannot be read from a stdin stream, because it needs to have the four
auxiliary binary files generated by hmmpress
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.
- Help; print a brief reminder of command line usage and all available
- -o <f>
- Direct the main human-readable output to a file <f> instead
of the default stdout.
- --tblout <f>
- Save a simple tabular (space-delimited) file summarizing the per-hit
output, with one data line per homologous target model hit 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.
- Use accessions instead of names in the main output, where available for
profiles and/or sequences.
- Omit the alignment section from the main output. This can greatly reduce
the output volume.
- 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
- --textw <n>
- Set the main output's line length limit to <n> characters per
line. The default is 120.
Reporting thresholds control which hits are reported in output files (the main
, and --dfamtblout
). Hits are ranked by
statistical significance (E-value).
- -E <x>
- Report target profiles 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 profiles
with a bit score of >= <x>.
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. In
, which does not have any alignment output (like
), inclusion thresholds have little effect. They only affect what
hits get marked as significant (!) or 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. It would be
unusual to use bit score thresholds with hmmscan, because you don't
expect a single score threshold to work for different profiles; different
profiles have slightly different expected score distributions.
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.
- 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.
- 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.
- Use the TC (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
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
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.
- Turn off (nearly) all filters, including the bias filter, and run full
Forward/Backward postprocessing on most of the target sequence. In
contrast to hmmscan, where this flag really does turn off the
filters entirely, the --max flag in nhmmscan 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 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>
- Set the P-value threshold for the Viterbi filter step. The default is
- --F3 <x>
- Set the P-value threshold for the Forward filter step. The default is
- 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.
- 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.
- --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 an arbitrarily chosen seed.
- --qformat <s>
- Assert that input query seqfile is in format <s>,
bypassing format autodetection. Common choices for <s>
include: fasta, embl, genbank. Alignment formats also
work; common choices include: stockholm, a2m, afa,
psiblast, clustal, phylip. For more information, and
for codes for some less common formats, see main documentation. The string
<s> is case-insensitive ( fasta or FASTA both
- --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.
- --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.
- Only search the top strand. By default both the query sequence and its
reverse-complement are searched.
- 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>. On
multicore machines, the default is 2. You can also control this number by
setting an environment variable, HMMER_NCPU. There is also a master
thread, so the actual number of threads that HMMER spawns is
This option is not available if HMMER was compiled with POSIX threads
support turned off.
- 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)
(Only available if optional MPI support was enabled at compile-time.)
- Run under MPI control with master/worker parallelization (using
mpirun, for example, or equivalent). Only available if optional MPI
support was enabled at compile-time.
(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 (http://hmmer.org/).
Copyright (C) 2018 Howard Hughes Medical Institute.
Freely distributed under the BSD open source license.
For additional information on copyright and licensing, see the file called
COPYRIGHT in your HMMER source distribution, or see the HMMER web page