NAME

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

SYNOPSIS

       pfscan [ -abflLrsuxy ] [ seq-file | - ]
                   [ profile-library-file | - ]    [L=#] [W=#]

DESCRIPTION

       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 -a, -l, -L, -r, -u, -s, -x, -y and -z.  seq-file
       contains a sequence in EMBL/SWISS-PROT format (assumed by default) or in Pearson/Fasta format  (indicated
       by  option  -f).   profile-library-file  contains a library of profiles in PROSITE format.  pfscan can be
       used as a filter if - is used instead of one of the input filenames.

OPTIONS

       -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.

       -l     Indicate 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 that 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.

       -r     Use raw scores rather than normalized scores for match selection. Normalized scores  will  not  be
              listed in the output.

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

       -u     Forces DISJOINT=UNIQUE.

       -x     List profile-sequence alignments in pftools PSA format.

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

PARAMETERS

       L=#    Cut-off  level  to  be  used for match selection.  If level L is not specified in the profile, the
              next higher (if L is negative) or next lower (if L is positive) level specified is used instead.

       W=#    Output width.  Output lines will be truncated after W characters.  Default: W=132.

EXAMPLES

       (1)    pfscan -s GTPA_HUMAN prosite13.prf

              Scans the human GAP protein for matches to profiles in PROSITE release  13.   GTPA_HUMAN  contains
              the  SWISS-PROT  entry  P20936|GTPA_HUMAN.   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 CVPBR322 ecp.prf L=2

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

AUTHOR

       Philipp Bucher
       Philipp.Bucher@isrec.unil.ch