xenial (1) hmmsearch.1.gz

Provided by: hmmer_3.1b2-2_amd64 bug

NAME

       hmmsearch - search profile(s) against a sequence database

SYNOPSIS

       hmmsearch [options] <hmmfile> <seqdb>

DESCRIPTION

       hmmsearch  is  used  to  search  one  or  more profiles against a sequence database.  For each profile in
       <hmmfile>, use that query profile to search the target database  of  sequences  in  <seqdb>,  and  output
       ranked  lists  of the sequences with the most significant matches to the profile.  To build profiles from
       multiple alignments, see hmmbuild.

       Either the query <hmmfile> or the target <seqdb> may be '-' (a dash character), in which case  the  query
       profile  or target database input will be read from a <stdin> pipe instead of from a file. Only one input
       source can come through <stdin>, not both.  An exception is that if the <hmmfile> contains more than  one
       profile  query,  then  <seqdb>  cannot  come  from  <stdin>, because we can't rewind the streaming target
       database to search it with another profile.

       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.

       -A <f> Save  a  multiple alignment of all significant hits (those satisfying inclusion thresholds) to the
              file <f>.

       --tblout <f>
              Save a simple tabular (space-delimited) file summarizing the per-target output, with one data line
              per homologous target sequence 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.

       --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 CONTROLLING REPORTING THRESHOLDS

       Reporting thresholds control which hits are reported in output files  (the  main  output,  --tblout,  and
       --domtblout).   Sequence hits and domain hits are ranked by statistical significance (E-value) and output
       is generated in two sections called per-target and per-domain output. In per-target output,  by  default,
       all  sequence hits with an E-value <= 10 are reported. In the per-domain output, for each target that has
       passed per-target reporting thresholds,  all  domains  satisfying  per-domain  reporting  thresholds  are
       reported.  By  default, these are domains with conditional E-values of <= 10. The following options allow
       you to change the default E-value reporting thresholds, or to use bit score thresholds instead.

       -E <x> In the per-target output, report target sequences 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 sequences with a  bit
              score of >= <x>.

       --domE <x>
              In  the  per-domain  output,  for  target  sequences  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-target  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, or
       marked as significant ("!") as opposed to 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.  By default this option is unset.

       --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, use a bit score of >= <x> as the per-domain inclusion threshold.

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 TC (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.

OPTIONS CONTROLLING 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  a
              randomly chosen seed.

       --tformat <s>
              Assert  that  the target sequence database 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.

       --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 at compile-time 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