man hmmscan (1): search protein sequence(s) against a protein profile database

SYNOPSIS

hmmscan [options] <hmmdb> <seqfile>

DESCRIPTION

hmmscan is used to search protein sequences against collections of protein 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 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.

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-target output, with one data line per homologous target model found.

--domtblout <f>

Save a simple tabular (space-delimited) file summarizing the per-domain output, with one data line per homologous domain detected in a query sequence for each homologous model.

--pfamtblout <f>

Save an especially succinct tabular (space-delimited) file summarizing the per-target output, with one data line per homologous target model found.

--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 --domtblout).

-E <x>

In the per-target output, 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 per-profile output on E-value, instead report target profiles with a bit score of >= <x>.

--domE <x>

In the per-domain output, for target profiles that have already satisfied the per-profile reporting threshold, report individual domains with a conditional E-value of <= <x>. The default is 10.0. A conditional E-value means the expected number of additional false positive domains in the smaller search space of those comparisons that already satisfied the per-profile reporting threshold (and thus must have at least one homologous domain already).

--domT <x>

Instead of thresholding per-domain output on E-value, instead report domains 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 hmmscan, which does not have any alignment output (like hmmsearch or phmmer) nor any iterative search steps (like jackhmmer), inclusion thresholds have little effect. They only affect what domains get marked as significant (!) or questionable (?) in domain output.

--incE <x>

Use an E-value of <= <x> as the per-target 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, instead use a bit score of >= <x> as the per-target 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.

--incdomE <x>

Use a conditional E-value of <= <x> as the per-domain inclusion threshold, in targets that have already satisfied the overall per-target inclusion threshold. The default is 0.01.

--incdomT <x>

Instead of using E-values, instead use a bit score of >= <x> as the per-domain inclusion threshold. As with --incT above, it would be unusual to use a single bit score threshold in hmmscan.

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. Each thresholding option has two scores: the per-sequence threshold <x1> and the per-domain threshold <x2> These act as if -T<x1> --incT<x1> --domT<x2> --incdomT<x2> has been applied specifically using each model's curated thresholds.

--cut_ga

Use the GA (gathering) bit scores in the model to set per-sequence (GA1) and per-domain (GA2) reporting and inclusion thresholds. GA thresholds are generally considered to be the reliable curated thresholds defining family membership; for example, in Pfam, these thresholds define what gets included in Pfam Full alignments based on searches with Pfam Seed models.

--cut_nc

Use the NC (noise cutoff) bit score thresholds in the model to set per-sequence (NC1) and per-domain (NC2) reporting and inclusion thresholds. NC thresholds are generally considered to be the score of the highest-scoring known false positive.

--cut_tc

Use the NC (trusted cutoff) bit score thresholds in the model to set per-sequence (TC1) and per-domain (TC2) reporting and inclusion thresholds. TC thresholds are generally considered to be the score of the lowest-scoring known true positive that is above all known false positives.

CONTROL OF THE ACCELERATION PIPELINE

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. 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.

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 all filters, including the bias filter, and run full Forward/Backward postprocessing on every target. This 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.

--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>

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.

--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.

--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.