pfsearch - search a protein or DNA sequence library for sequence segments
matching a profile
- pfsearch
- [ -abdfhlLmruksvxyz ] [ -C cut_off ] [
-M mode_nb ] [ -W width ] [ profile |
- ] [ sequence_library | - ] [ parameters
]
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.
- 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
- -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
- 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.
- (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.
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.
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.
pfscan(1),
pfmake(1),
psa2msa(1),
psa(5),
xpsa(5)
The
pftools package was developed by Philipp Bucher.
Any comments or suggestions should be addressed to
<
[email protected]>.