Provided by: hmmer_3.1b1-3_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

       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