Provided by: hmmer_3.1b1-3_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, 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

       Copyright (C) 2013 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