nhmmscan - Man Page

search nucleotide sequence(s) against a nucleotide profile database


hmmscan [options] <hmmdb> <seqfile>


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 hmmscan. 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 those 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 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.


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 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.


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 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.

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.


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.


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


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 the query sequence file is in format <s>. Accepted formats include fasta, embl, genbank, ddbj, uniprot, stockholm, pfam, a2m, and afa. The default is to autodetect the format of the file.

--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>. 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 for your site or machine for some reason.


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.)


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 ().


Eddy/Rivas Laboratory
Janelia Farm Research Campus
19700 Helix Drive
Ashburn VA 20147 USA


February 2015 HMMER 3.1b2 HMMER Manual