pfscan - scan a protein or DNA sequence with a profile library
- pfscan
- [ -abdfhlLmruksvxyz ] [ -C cut_off ] [ -M
mode_nb ] [ -W width ] [ sequence | - ]
[ profile_library | - ] [ parameters ]
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.
- 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
- -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
- 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.
- (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.
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.
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.
The pftools package was developed by Philipp Bucher.
Any comments or suggestions should be addressed to
<pftools@sib.swiss>.