Provided by: hmmer_3.1b2+dfsg-5ubuntu1_amd64 bug

NAME

       phmmer - search protein sequence(s) against a protein sequence database

SYNOPSIS

       phmmer [options] <seqfile> <seqdb>

DESCRIPTION

       phmmer  is  used  to search one or more query protein sequences against a protein sequence
       database.  For each query sequence in <seqfile>, use that sequence to  search  the  target
       database  of  sequences in <seqdb>, and output ranked lists of the sequences with the most
       significant matches to the query.

       Either the query <seqfile> or the target <seqdb> may be '-' (a dash character),  in  which
       case the query sequences 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 <seqfile> contains more than one query sequence, then <seqdb> cannot come from
       <stdin>, because we can't rewind the streaming target database to search it  with  another
       query.

       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> in Stockholm format.

       --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 SCORING SYSTEM

       The  probability  model in phmmer is constructed by inferring residue probabilities from a
       standard 20x20 substitution score matrix, plus two  additional  parameters  for  position-
       independent gap open and gap extend probabilities.

       --popen <x>
              Set the gap open probability for a single sequence query model to <x>.  The default
              is 0.02.  <x> must be >= 0 and < 0.5.

       --pextend <x>
              Set the gap extend probability for a single  sequence  query  model  to  <x>.   The
              default is 0.4.  <x> must be >= 0 and < 1.0.

       --mx <s>
              Obtain  residue alignment probabilities from the built-in substitution matrix named
              <s>.  Several standard matrices are built-in, and do  not  need  to  be  read  from
              files.   The  matrix  name  <s>  can  be  PAM30,  PAM70,  PAM120, PAM240, BLOSUM45,
              BLOSUM50, BLOSUM62, BLOSUM80, or BLOSUM90.  Only  one  of  the  --mx  and  --mxfile
              options may be used.

       --mxfile <mxfile>
              Obtain  residue  alignment  probabilities  from  the  substitution  matrix  in file
              <mxfile>.  The default score matrix is BLOSUM62 (this matrix is internal  to  HMMER
              and  does not have to be available as a file).  The format of a substitution matrix
              <mxfile> is the standard format  accepted  by  BLAST,  FASTA,  and  other  sequence
              analysis software.  Only one of the --mx and --mxfile options may be used.

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 CONTROLLING INCLUSION THRESHOLDS

       Inclusion  thresholds  are stricter than reporting thresholds. They control which hits are
       included in any output multiple alignment (the -A option) and which domains are 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.  By default this option is unset.

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, slowest  but  most  accurate.
       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.

       Essentially  the  only  free  parameters that control HMMER's heuristic filters are the P-
       value thresholds controlling the expected fraction of nonhomologous  sequences  that  pass
       the  filters.  Setting  the  default  thresholds  higher  will pass a higher proportion of
       nonhomologous sequence, increasing  sensitivity  at  the  expense  of  speed;  conversely,
       setting  lower  P-value  thresholds will pass a smaller proportion, decreasing sensitivity
       and increasing speed. Setting a filter's P-value threshold to 1.0 means  it  will  passing
       all sequences, and effectively disables the filter.

       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  Maximum sensitivity.  Turn off all filters, including the bias filter, and run full
              Forward/Backward  postprocessing  on  every  target.  This  increases   sensitivity
              slightly, at a large cost in speed.

       --F1 <x>
              First  filter  threshold;  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>
              Second  filter  threshold;  set  the P-value threshold for the Viterbi filter step.
              The default is 0.001.

       --F3 <x>
              Third filter threshold; 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.

OPTIONS CONTROLLING E-VALUE CALIBRATION

       Estimating  the  location  parameters  for the expected score distributions for MSV filter
       scores, Viterbi filter scores, and Forward scores requires  three  short  random  sequence
       simulations.

       --EmL <n>
              Sets the sequence length in simulation that estimates the location parameter mu for
              MSV filter E-values. Default is 200.

       --EmN <n>
              Sets the number of sequences in simulation that estimates the location parameter mu
              for MSV filter E-values. Default is 200.

       --EvL <n>
              Sets the sequence length in simulation that estimates the location parameter mu for
              Viterbi filter E-values. Default is 200.

       --EvN <n>
              Sets the number of sequences in simulation that estimates the location parameter mu
              for Viterbi filter E-values. Default is 200.

       --EfL <n>
              Sets  the  sequence  length in simulation that estimates the location parameter tau
              for Forward E-values. Default is 100.

       --EfN <n>
              Sets the number of sequences in simulation that estimates  the  location  parameter
              tau for Forward E-values. Default is 200.

       --Eft <x>
              Sets  the  tail  mass fraction to fit in the simulation that estimates the location
              parameter tau for Forward evalues. Default is 0.04.

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>
              Seed the random number generator with <n>, an integer >= 0.   If  <n>  is  >0,  any
              stochastic  simulations  will  be reproducible; the same command will give the same
              results.  If <n> is 0, the random  number  generator  is  seeded  arbitrarily,  and
              stochastic  simulations will vary from run to run of the same command.  The default
              seed is 42.

       --qformat <s>
              Declare that the input <seqfile> 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.

       --tformat <s>
              Declare that the input <seqdb> 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) 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