Provided by: pftools_3.2.12-1_amd64 bug


       pfscan - scan a protein or DNA sequence with a profile library


       pfscan    [  -abdfhlLmruksvxyz ] [ -C cut_off ] [ -M mode_nb ] [ -W width ] [ sequence | -
                 ] [ profile_library | - ] [ parameters ]


       pfscan compares a protein or nucleic acid sequence against a profile 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 'sequence' contains a sequence in EMBL/SWISS-
       PROT format (assumed by default) or in Pearson/Fasta format (indicated by option -f).  The
       'profile_library'  file  contains  a  library  of  profiles  in PROSITE format.  If '-' is
       specified instead of one of the  filenames,  the  corresponding  data  is  read  from  the
       standard input.


              Input query sequence.
              This  DNA  or  protein  sequence will be used to search for matches to a library of
              PROSITE profiles.
              The content of  the  file  must  be  either  in  EMBL/SWISS-PROT  (default)  or  in
              Pearson/Fasta  format  (option  -f).   If the filename is replaced by a '-', pfscan
              will read the input sequence from stdin.

              Library of PROSITE profiles.
              This file should contain one or several PROSITE profiles, against which  the  query
              sequence  will be matched.  Each entry in this library should be separated from the
              next by a line containing only the '//' code.  If the filename  is  replaced  by  a
              '-', pfscan will read the profile library from stdin.

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

       -b     Search the complementary strand of the DNA sequence as well.

       -f     Input sequence 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,  pfscan
              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.

       -u     Forces DISJOINT=UNIQUE.

       -C cut_off
              Cut-off level to be used for match selection.
              The  value  of  'cut_off'  should  be  the  numerical identifier of a cut-off level
              defined in the profile.  The raw or normalized score of this  level  will  then  be
              used to include profile to sequence matches in the output list.
              If  the  specified level does not exist in the profile, the next higher (if cut_off
              is negative) or next lower (if cut_off is positive) level defined is used instead.
              Type: integer
              Default: 0

       -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 profile description length.
              If  this  option  is set, the description of the profile on the header line will be
              limited in length. If the  match  information  is  longer  than  the  output  width
              specified  using  option  -W, the profile description will not be printed. Else the
              description will be truncated to fit the -W value.
              By default, the profile 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.

       L=#    Cut-off level.
              Use option -C instead, not -L.

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


       (1)    pfscan -s GTPA_HUMAN prosite13.prf

              Scans  the  human  GAP  protein for matches to profiles in PROSITE release 13.  The
              file 'GTPA_HUMAN' contains the SWISS-PROT  entry  P20936|GTPA_HUMAN.   The  profile
              library  file  'prosite13.prf'  contains all profile entries of PROSITE release 13.
              The output is a Pearson/Fasta-formatted sequence library  containing  all  sequence
              regions of the input sequence matching a profile in the profile library.

       (2)    pfscan -by -C 2 CVPBR322 ecp.prf

              Scans  both  strands  of plasmid PBR322 for high-scoring (level 2) E. coli promoter
              matches.  The sequence file 'CVPBR322' contains EMBL  entry  J01749|CVPBR322.   The
              profile  library  file  'ecp.prf'  contains  a  profile for E. coli promoters.  The
              output includes profile-sequence alignments in a human-friendly format.


       On successful completion of its task, pfscan 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.


       If  the  match  selection  is  based  on  normalized  scores (i.e.  option -r is not set),
       rounding errors can lead to the exclusion of some matches even if the raw score  is  above
       or equal to the specified cut-off level score.


       pfsearch(1), pfmake(1), psa(5), xpsa(5)


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