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