xenial (1) nhmmscan.1.gz

Provided by: hmmer_3.1b2-2_amd64 bug

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.

              (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 ().

       Copyright (C) 2015 Howard Hughes Medical Institute.
       Freely distributed under the GNU General Public License (GPLv3).

       For additional information on copyright and licensing, see the file called COPYRIGHT in your HMMER source
       distribution, or see the HMMER web page ().

AUTHOR

       Eddy/Rivas Laboratory
       Janelia Farm Research Campus
       19700 Helix Drive
       Ashburn VA 20147 USA
       http://eddylab.org