Provided by: hmmer2_2.3.2-7ubuntu1_amd64 bug

NAME

       hmm2search - search a sequence database with a profile HMM

SYNOPSIS

       hmm2search [options] hmmfile seqfile

DESCRIPTION

       hmm2search  reads  an  HMM  from  hmmfile  and  searches seqfile for significantly similar
       sequence matches.

       seqfile will be looked for first in the current working directory,  then  in  a  directory
       named  by the environment variable BLASTDB.  This lets users use existing BLAST databases,
       if BLAST has been configured for the site.

       hmm2search may take minutes or even hours to run, depending on the size  of  the  sequence
       database. It is a good idea to redirect the output to a file.

       The  output  consists  of  four  sections:  a ranked list of the best scoring sequences, a
       ranked list of the best scoring domains, alignments for all the best scoring domains,  and
       a  histogram  of  the  scores.  A sequence score may be higher than a domain score for the
       same sequence if there is more than one domain in the sequence; the sequence  score  takes
       into account all the domains.  All sequences scoring above the -E and -T cutoffs are shown
       in the first list, then every domain found in this list is shown in  the  second  list  of
       domain  hits.   If  desired,  E-value  and bit score thresholds may also be applied to the
       domain list using the --domE and --domT options.

OPTIONS

       -h     Print brief help; includes version number and summary  of  all  options,  including
              expert options.

       -A <n> Limits  the  alignment  output  to the <n> best scoring domains.  -A0 shuts off the
              alignment output and can be used to reduce the size of output files.

       -E <x> Set the E-value cutoff for the per-sequence ranked hit list to <x>, where <x> is  a
              positive  real  number.  The  default is 10.0. Hits with E-values better than (less
              than) this threshold will be shown.

       -T <x> Set the bit score cutoff for the per-sequence ranked hit list to <x>, where <x>  is
              a  real  number.   The  default  is negative infinity; by default, the threshold is
              controlled by E-value and not by bit score.   Hits  with  bit  scores  better  than
              (greater than) this threshold will be shown.

       -Z <n> Calculate  the  E-value  scores  as  if  we  had  seen  a  sequence database of <n>
              sequences. The default is the number  of  sequences  seen  in  your  database  file
              <seqfile>.

EXPERT OPTIONS

       --compat
              Use  the  output  format  of HMMER 2.1.1, the 1998-2001 public release; provided so
              2.1.1 parsers don't have to be rewritten.

       --cpu <n>
              Sets the maximum number of CPUs that the program will run on. The default is to use
              all  CPUs  in  the  machine.  Overrides  the  HMMER_NCPU environment variable. Only
              affects threaded versions of HMMER (the default on most systems).

       --cut_ga
              Use Pfam GA (gathering threshold)  score  cutoffs.   Equivalent  to  --globT  <GA1>
              --domT  <GA2>,  but  the  GA1 and GA2 cutoffs are read from the HMM file. hmm2build
              puts these cutoffs there if the alignment file was  annotated  in  a  Pfam-friendly
              alignment  format  (extended  SELEX  or  Stockholm  format)  and  the  optional  GA
              annotation line was present. If these cutoffs are not set in the HMM file, --cut_ga
              doesn't work.

       --cut_tc
              Use  Pfam  TC  (trusted  cutoff)  score cutoffs. Equivalent to --globT <TC1> --domT
              <TC2>, but the TC1 and TC2 cutoffs are read from the HMM file. hmm2build puts these
              cutoffs  there  if  the  alignment  file was annotated in a Pfam-friendly alignment
              format (extended SELEX or Stockholm format) and the optional TC annotation line was
              present. If these cutoffs are not set in the HMM file, --cut_tc doesn't work.

       --cut_nc
              Use Pfam NC (noise cutoff) score cutoffs. Equivalent to --globT <NC1> --domT <NC2>,
              but the NC1 and NC2 cutoffs are read  from  the  HMM  file.  hmm2build  puts  these
              cutoffs  there  if  the  alignment  file was annotated in a Pfam-friendly alignment
              format (extended SELEX or Stockholm format) and the optional NC annotation line was
              present. If these cutoffs are not set in the HMM file, --cut_nc doesn't work.

       --domE <x>
              Set  the  E-value  cutoff for the per-domain ranked hit list to <x>, where <x> is a
              positive real number.  The default is infinity; by  default,  all  domains  in  the
              sequences  that  passed the first threshold will be reported in the second list, so
              that the number of domains reported in the per-sequence list is consistent with the
              number that appear in the per-domain list.

       --domT <x>
              Set  the bit score cutoff for the per-domain ranked hit list to <x>, where <x> is a
              real number. The default is negative infinity;  by  default,  all  domains  in  the
              sequences  that  passed the first threshold will be reported in the second list, so
              that the number of domains reported in the per-sequence list is consistent with the
              number  that  appear  in the per-domain list.  Important note: only one domain in a
              sequence is absolutely controlled by this parameter, or by --domT.  The second  and
              subsequent  domains  in a sequence have a de facto bit score threshold of 0 because
              of the details of how HMMER works. HMMER requires at least  one  pass  through  the
              main  model  per  sequence;  to  do  more  than one pass (more than one domain) the
              multidomain alignment must have a better score than the  single  domain  alignment,
              and  hence  the  extra domains must contribute positive score. See the Users' Guide
              for more detail.

       --forward
              Use the Forward algorithm instead of the Viterbi algorithm to  determine  the  per-
              sequence  scores.  Per-domain scores are still determined by the Viterbi algorithm.
              Some have argued that Forward is a more sensitive algorithm  for  detecting  remote
              sequence homologues; my experiments with HMMER have not confirmed this, however.

       --informat <s>
              Assert  that  the  input  seqfile  is  in  format  <s>; do not run Babelfish format
              autodection. This increases the reliability of the program  somewhat,  because  the
              Babelfish  can  make  mistakes;  particularly  recommended  for  unattended,  high-
              throughput runs of HMMER. Valid format strings include FASTA, GENBANK,  EMBL,  GCG,
              PIR,  STOCKHOLM,  SELEX,  MSF,  CLUSTAL,  and  PHYLIP.  See  the User's Guide for a
              complete list.

       --null2
              Turn off the post hoc second null model. By default, each alignment is rescored  by
              a postprocessing step that takes into account possible biased composition in either
              the HMM or the target sequence.  This is almost  essential  in  database  searches,
              especially  with  local  alignment  models.  There is a very small chance that this
              postprocessing might remove real matches, and in these cases  --null2  may  improve
              sensitivity  at  the  expense of reducing specificity by letting biased composition
              hits through.

       --pvm  Run on a Parallel Virtual Machine (PVM). The  PVM  must  already  be  running.  The
              client program hmm2search-pvm must be installed on all the PVM nodes.  Optional PVM
              support must have been compiled into HMMER.

       --xnu  Turn on XNU filtering of target protein sequences. Has no effect  on  nucleic  acid
              sequences.  In  trial  experiments,  --xnu  appears  to  perform less well than the
              default post hoc null2 model.

SEE ALSO

       Master man page, with full list of and guide to the individual man pages: see hmmer2(1).

       For        complete        documentation,        see        the         user         guide
       (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf);  or  see  the  HMMER web
       page, http://hmmer.janelia.org/.

COPYRIGHT

       Copyright (C) 1992-2003 HHMI/Washington University School of Medicine.
       Freely distributed under the GNU General Public License (GPL).
       See the file COPYING in your distribution for details on redistribution conditions.

AUTHOR

       Sean Eddy
       HHMI/Dept. of Genetics
       Washington Univ. School of Medicine
       4566 Scott Ave.
       St Louis, MO 63110 USA
       http://www.genetics.wustl.edu/eddy/