Provided by: pftools_3.2.12-1_amd64 bug


       pfsearch  -  search  a  protein  or  DNA sequence library for sequence segments matching a


       pfsearch  [ -abdfhlLmruksvxyz ] [ -C cut_off ] [ -M mode_nb ] [ -W width ] [ profile | - ]
                 [ sequence_library | - ] [ parameters ]


       pfsearch  compares  a query profile against a DNA or protein sequence library.  The result
       is an unsorted list of profile-sequence matches written to the standard output.  A variety
       of  output  formats  containing  different  information  can  be specified via the options
       -l, -L, -r, -k, -s, -x, -y and -z.  The file  'profile'  contains  a  profile  in  PROSITE
       format.  The 'sequence_library' file contains a sequence library in EMBL/SWISS-PROT format
       (assumed by default) or in Pearson/Fasta format (indicated  by  option  -f).   If  '-'  is
       specified  instead  of  one  of  the  filenames,  the  corresponding data is read from the
       standard input.


              Input query profile.
              The PROSITE profile contained in this file will be used to search  for  profile  to
              sequence matches in a biological sequence library. If the filename is replaced by a
              '-', pfsearch will read the profile from stdin.

              Library of DNA or protein sequences.
              This file should contain one or several EMBL/SWISS-PROT (default) or  Pearson/Fasta
              (option  -f)  formatted  DNA  or  protein  sequences. The program pfsearch tries to
              identify matches between the input profile and all  individual  sequences  of  this
              library.  If  the  filename  is  replaced by a '-', pfsearch will read the sequence
              library from stdin.

       -a     Report optimal alignment scores for all sequences regardless of the cut-off  value.
              This option simultaneously forces DISJOINT=UNIQUE.

       -b     Search the complementary strands of DNA sequences as well.

       -f     Input sequence library is in Pearson/Fasta format.

       -h     Display usage help text.

       -l     Indicate  the value of the highest cut-off level exceeded by the match score in the
              output list.

       -L     Indicate by character string the highest cut-off level exceeded by the match  score
              in the output list.

              Note:  The  generalized  profile  format  includes a text string field to specify a
                     name for a cut-off level. The -L option causes the program  to  display  the
                     first   two   characters   of  this  text  string  (usually  something  like
                     '!', '?', '??', etc.) at the beginning of each match description.

       -m     Report individual matches for circular profiles.
              If the profile is circular, each match between a sequence  and  a  profile  can  be
              composed  of  a  stretch of individual matches of the profile. By default, pfsearch
              reports  only  the  total  matched  region.  When  this  option  is  set,  detailed
              information for each individual match will be output as well.

              Note:  The  scoring  system  for  most circular profiles has been optimized to find
                     total matches, therefore the normalized scores of individual  matches  of  a
                     circular profile to a sequence should be considered with caution.

       -r     Use  raw  scores  rather than normalized scores for match selection. The normalized
              score is not printed, this option is useful to create raw score lists  to  be  used
              with pfscale(1).

       -u     Forces DISJOINT=UNIQUE.

       -C cut_off
              Cut-off value to be used for match selection.
              The  value  of  'cut_off'  overwrites the level zero cut-off value specified in the
              An integer argument is interpreted as a raw score value, a decimal  argument  as  a
              normalized score value.
              Default: profile level 0 cut-off value (normalized score if present)

              Note:  Compared  to  release  2.2,  an  integer  value  does  not  force option -r.
                     Normalized scores will still be listed in output if an  integer  cut-off  is
                     specified on the command line but cut-off level computation will be based on
                     raw score.

       -M mode_nb
              Normalization mode to use for score computation.
              The 'mode_nb' specifies which normalization mode defined in the profile  should  be
              used  to compute the normalized scores for profile to sequence matches. This option
              will override the profile's PRIORITY parameter.
              If the specified normalization mode does not exist in the profile, an error message
              will be output to standard error and the search is interrupted.
              Type: integer
              Default: lowest priority mode defined in the profile

   Output modifiers
       -d     Limit sequence description length.
              If  this  option is set, the description of the sequence on the header line will be
              limited in length. If the  match  information  is  longer  than  the  output  width
              specified  using  option -W, the sequence description will not be printed. Else the
              description will be truncated to fit the -W value.
              By default, the sequence description is not truncated. This option can not be  used
              when option -k is set.

       -k     Use xpsa(5) headers for output.
              When  this  option  is  set, all output types (see below) will use an xpsa(5) style
              header line. This format uses keyword=value pairs to output  alignment  parameters.
              It is useful to transfer information between different sequence alignment tools.

       -s     List  the  sequences  of  the  matched  regions  as  well.   The  output  will be a
              Pearson/Fasta-formatted sequence library.

       -v     Suppress sequence/profile parsing warnings.  If  this  option  is  set  no  warning
              messages  will  be  printed  on  stderr.   Only fatal errors will be reported. This
              option should be used with caution.

       -x     List  profile-sequence  alignments  in  psa(5)  format.   Please   refer   to   the
              corresponding man page for more information.

       -y     Display alignments between the profile and the matched sequence regions in a human-
              friendly pairwise alignment format.

       -z     Indicate starting and ending position of the  matched  profile  range.  The  latter
              position  will  be given as a negative offset from the end of the profile. Thus the
              range [    1,    -1] means entire profile.

       -W width
              Set alignment output width.
              The value of 'width' specifies how many residues will be output on  one  line  when
              any of the -s, -x or -y options is set.
              Type: integer
              Default: 60


       Note:  for  backwards  compatibility,  release  2.3  of the pftools package will parse the
              version 2.2 style parameters, but these are deprecated and the corresponding option
              (refer to the options section) should be used instead.

       C=#    Cut-off value.
              Use option -C instead.

       W=#    Output width.
              Use option -W instead.


       (1)    pfsearch -f -C 6.0 sh3.prf sh3.seq

              Searches  the  Pearson/Fasta-formatted  protein  sequence library 'sh3.seq' for SH3
              domains with a cut-off value of 6.0 normalized score  units.   The  file  'sh3.seq'
              contains  20  SH3  domain-containing  protein sequences from SWISS-PROT release 32.
              The file 'sh3.prf' contains the PROSITE entry SH3/PS50002.

       (2)    pfsearch -bx ecp.prf CVPBR322 | psa2msa -du | readseq -p -fMSF > ecp.msf

              Generates a multiple sequence alignment  of potential E.  coli  promoters  on  both
              strands  of  plasmid  pBR322.   The  file  'ecp.prf' contains a profile for E. coli
              promoters.  The file 'CVPBR322'
               contains EMBL entry J01749|CVPBR322.  The result file  'ecp.msf'  can  further  be
              processed by GCG programs accepting MSF files as input.


       On  successful completion of its task, pfsearch will return an exit code of 0. If an error
       occurs, a diagnostic message will be output on standard error and the exit  code  will  be
       different  from 0. When conflicting options where passed to the program but the task could
       nevertheless be completed, warnings will be issued on standard error.


       The use of normalized scores as cut-off values can lead  to  a  different  behaviour  when
       compared  to  raw scores. This is due to the inherent rounding inaccuracy of real numbers.
       The normalized scores used as cut-offs should be rounded down in order to circumvent  this


       pfscan(1), pfmake(1), psa2msa(1), psa(5), xpsa(5)


       The pftools package was developed by Philipp Bucher.
       Any comments or suggestions should be addressed to <>.