Ubuntu Manpage: nhmmscan - search nucleotide sequence(s) against a nucleotide profile database

name
synopsis
description
options
options for controlling output
options for reporting thresholds
options for inclusion thresholds
options for model-specific score thresholding
control of the acceleration pipeline
other options
see also
copyright
author

NAME

       nhmmscan - search nucleotide sequence(s) against a nucleotide profile database

SYNOPSIS

       hmmscan [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 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.

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 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.

--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 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.

--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 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.