Provided by: hmmer_3.4+dfsg-2_amd64 
NAME
nhmmscan - search DNA sequence(s) against a DNA profile database
SYNOPSIS
nhmmscan [options] hmmdb seqfile
DESCRIPTION
nhmmscan 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 sequence.
The seqfile 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.
The hmmdb needs to be press'ed using hmmpress before it can be searched with nhmmscan. This creates four
binary files, suffixed .h3{fimp}.
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.
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.
--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.
--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 FOR 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 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>.
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. In
nhmmscan, which does not have any alignment output (like nhmmer), 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.
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 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 organism.
CONTROL OF 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 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 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.
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.
--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
work).
--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.
--watson
Only search the top strand. By default both the query sequence and its reverse-complement are
searched.
--crick
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>. The default is 0, meaning off (no thread-level
parallelization), because nhmmscan is typically i/o bound and the extra overhead of our current
multithreaded implementation isn't worthwhile. 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 at least <n>+1.
This option is not available if HMMER was compiled with POSIX threads support turned off.
--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 under MPI control with master/worker parallelization (using mpirun, for example, or
equivalent). 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 (http://hmmer.org/).
COPYRIGHT
Copyright (C) 2023 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 (http://hmmer.org/).
AUTHOR
http://eddylab.org
HMMER 3.4 Aug 2023 nhmmscan(1)