pfscale - fit parameters of an extreme-value distribution to a
profile score list
- pfscale
- [ -hl ] [ -L log_base ] [ -M mode_nb ]
[ -N db_size ] [ -P upper_limit ] [ -Q
lower_limit ] [ score_list | - ] [ profile ] [
parameters ]
pfscale fits the two parameters of an extreme-value
distribution to a sorted score distribution obtained by searching a sequence
database with a profile. The file 'score_list' is a sorted list of
profile match scores generated by pfsearch. If '-' is
specified instead of a filename, the score list is read from the standard
input. The result is written to the standard output.
If the original profile is given as the second argument, the
normalization function with the lowest mode number or the lowest priority
number specified within the profile will be updated such as to produce
-Log10 per-residue E-values. If the second argument is omitted, the output
consists of a header line containing the normalization parameters followed
by a modified score list, showing score rank, original raw
scores, log-cumulative frequencies and corresponding
normalized scores next to each other.
Note that this program implements the significance estimation
procedure for profile match scores described in Hofmann & Bucher (1995).
It has been used for the calculation of the normalization parameters of all
profiles in the PROSITE database.
- score_list
- Input score list.
The file must contain a sorted list of scores. The first field of each line
is considered as being a score, all other fields on the same line are
ignored. The different fields of each line should be delimited by
whitespaces. If the filename is replaced by a '-', pfscale
will read the score list from stdin.
- profile
- Optional profile file.
If a filename is specified, the profile will be parsed and either the lowest
priority mode or the mode number specified with option -M will be
scaled. All cut-off levels which use the specified mode number will also
be updated.
- -h
- Display usage help text.
- -l
- Remove output line length limit. Individual lines of the output profile
can exceed a length of 132 characters, removing the need to wrap them over
several lines.
- -L log_base
- Logarithmic base of the parameters of the estimated extreme-value
distribution. The parameters reported by pfscale are expressed as
logarithms and thus can be inserted directly into a linear normalization
function defined in a generalized profile.
Default: 10
- -M mode_nb
- Mode number to scale.
Defines which mode number (and implicitly which cut-off level) of the input
PROSITE profile should be scaled. This overrides the
default behaviour of scaling only the normalization mode with the lowest
priority (or lowest mode number). All cut-off levels defined in the
profile as using this mode number (via the MODE keyword) will be
updated as well.
- -N db_size
- Size of the database from which the input score list was derived. The
searched database is typically a shuffled version of a real protein or
nucleotide sequence database.
Default: 14147368 (size of SWISS-PROT release 30 and shuffled
derivatives of it).
- -P upper_limit
- Upper threshold of the probability range to which the extreme-value
distribution will be fitted. For instance: if N=10'000'000 and
P=0.0001 then profile match scores below rank 1000 in the sorted
input list (corresponding to occurrence probabilities > 0.0001) will be
ignored.
Default: 0.0001
- -Q lower_limit
- Lower threshold of the probability range to which the extreme-value
distribution will be fitted. For instance: if N=10'000'000 and
Q=0.000001 then profile match scores above rank 10 in the sorted
input list (corresponding to occurrence probabilities < 0.000001) will
be ignored.
Default: 0.000001
- 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=#
- Logarithmic base.
Use option -L instead.
- M=#
- Mode number.
Use option -M instead.
- N=#
- Database size.
Use option -N instead.
- P=#
- Upper probability threshold.
Use option -P instead.
- Q=#
- Lower probability threshold.
Use option -Q instead.
- (1)
- pfsearch -fr -C 200 sh3.prf shuffle20.seq | sort -nr |
pfscale -P 0.0001 -Q 0.000001 -
- derives score-normalization parameters for the SH3 domain profile in file
'sh3.prf'. The file 'shuffle20.seq' contains a
window-shuffled derivative of SWISS-PROT release 30 in
Pearson/Fasta format (window-size 20). Note that the implicit default of
N corresponds to the size of this database and thus needs not to be
specified on the command line. The cut-off value 200 for the
pfsearch(1) option -C will produce about 2000 matches
completely covering the range defined by the command line parameters
-P and -Q of pfscale. A suitable cut-off value has to
be guessed in advance by computing a few optimal alignment scores for
random sequences.
On successful completion of its task, pfscale 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.
Hofmann K & Bucher P. (1995). The FHA-domain: a nuclear
signalling domain found in protein kinases and transcription factors.
Trends Biochem. Sci. 20:47-349.
The pftools package was developed by Philipp Bucher.
Any comments or suggestions should be addressed to
<pftools@sib.swiss>.