Ubuntu Manpage: pfscan - scan a protein or DNA sequence with a profile library

NAME

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

SYNOPSIS

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

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
       -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.

OPTIONS

sequence
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.

profile_library
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

PARAMETERS

       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.

EXAMPLES

       (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.

EXIT CODE

       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.

BUGS

       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.

AUTHOR

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