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.
-Ccut_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.
-Mmode_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
Outputmodifiers-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.
-Wwidth
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
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