Provided by: pftools_3.2.12-1_amd64 
NAME
pfsearch - search a protein or DNA sequence library for sequence segments matching a
profile
SYNOPSIS
pfsearch [ -abdfhlLmruksvxyz ] [ -C cut_off ] [ -M mode_nb ] [ -W width ] [ profile | - ]
[ sequence_library | - ] [ parameters ]
DESCRIPTION
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.
OPTIONS
profile
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.
sequence_library
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
profile.
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
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.
C=# Cut-off value.
Use option -C instead.
W=# Output width.
Use option -W instead.
EXAMPLES
(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.
EXIT CODE
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.
BUGS
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
problem.
SEE ALSO
pfscan(1), pfmake(1), psa2msa(1), psa(5), xpsa(5)
AUTHOR
The pftools package was developed by Philipp Bucher.
Any comments or suggestions should be addressed to <pftools@sib.swiss>.