Provided by: pftools_3.2.12-1_amd64 
NAME
ptof - convert a protein profile into a frame-search profile
SYNOPSIS
ptof [ -hlr ] [ -B init/term_score ] [ -F frameshift ] [ -I insert_multiplier ] [ -X stop_codon ] [
-Y intron_open ] [ -Z intron_extend ] [ protein_profile | - ] [ parameters ]
DESCRIPTION
ptof converts a protein profile (generated for instance by pftools programs pfmake(1), gtop(1) or
htop(1)) into a so-called "frame-search profile". A frame-search profile is used to search an
"interleaved frame-translated" DNA sequence (generated by pftools program 2ft(1)) for occurrences of a
protein sequence motif. An "interleaved frame-translated" DNA sequence is an amino acid sequence
corresponding to the N-2 overlapping codons of a DNAsequence of length N. Note that in such a sequence,
the character 'O' is used to represent stop codons.
The conversion procedure works as follows: The protein profile is expanded in length by a factor of three
to accommodate three translated codons per original match position. Two dummy match positions are placed
between two consecutive significant match positions imported from the original profile. The original
insert positions are placed between pairs of adjacent dummy match positions. The initiation,
termination, and transition scores of the original insert positions are left unchanged; the insert
extension scores are divided by a factor of 3, or by the value of the command-line option -I. The two
insert positions flanking the significant match positions serve to accommodate frame-shift errors and
introns, respectively. The frame-shift insert position allows free insertion opening combined with a
high insert extension penalty (command-line option -F) whereas the intron insertion position has high
opening but low extension penalties (command line options -Y and -Z). The deletion opening and closing
penalties next to the significant match positions are set to values that ensure that the total cost of a
single-base deletion is the same as the cost of a single base-insertion at a frame-shift insert position.
Furthermore, the alphabet of the original profile is extended by the stop codon symbol 'O' which is
assigned a constant negative value (command-line option -X) at significant match positions, and zero at
dummy match positions. At insert positions, it is set to the average of the other insert extension
scores.
OPTIONS
protein_profile
Input protein profile.
The protein profile contained in this file will be converted into a frame-search profile. If the
filename is replaced by a '-', ptof will read the profile from stdin.
-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.
-r Frame-search parameters are given in normalized score units. This option will only be considered
if a linear normalization function with priority over all other normalization functions is
specified in the profile. In this case, the frame-search scores specified on the command line
will be divided by the slope (R2 parameter) of the normalization function. This option is
particularly useful for profiles which are already scaled in units that can be interpreted as
−Log(P)-values, e.g. bits.
-B init/term_score
Minimal initiation and termination score.
All internal and external initiation and termination scores will be set to this value if the
corresponding value in the original profile is lower than this value. This parameter is used to
impose a more local alignment behavior on the frame-search profile in order to deal with
discontinuities in DNA sequences (long introns, alternative splicing, chimeric clones, etc.)
Default: -50 (-0.5 with option -r)
-F frameshift
Frame-shift error penalty.
Default: -100 (-1.0 with option -r)
-I insert_multiplier
Insert score multiplier.
The values of the original insert extension scores will be multiplied by this factor in order to
compensate for the fact that a single amino acid corresponds to three overlapping codon positions
in the target sequence.
Default: 1/3
-X stop_codon
Stop codon penalty.
Default: -100 (-1.0 with option -r)
-Y intron_open
Intron opening penalty.
Default: -300 (-3.0 with option -r)
-Z intron_extend
Intron extension penalty.
Default: -1 (-0.01 with option -r)
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.
B=# Minimal initiation and termination score.
Use option -B instead.
F=# Frame-shift error penalty.
Use option -F instead.
I=# Insert score multiplier.
Use option -I instead.
X=# Stop codon penalty.
Use option -X instead.
Y=# Intron opening penalty.
Use option -Y instead.
Z=# Intron extension penalty.
Use option -Z instead.
EXAMPLES
(1) ptof -r -F -1.2 -I 0.6 -X -1.5 -B -0.5 sh3.prf > sh3.fsp
2ft - < R76849.seq | pfsearch -fy -C 5.0 sh3.fsp -
The protein domain profile in 'sh3.prf' is first converted into a frame-search profile 'sh3.fsp'.
Then both strands of the Fasta-formatted EST sequence in 'R76849.seq' (GenBank/EMBL-accession:
R76849) are converted into interleaved frame-translated protein sequences and searched for SH3
domains with the frame-search profile generated in the preceding step.
The output may be compared to the result of a more conventional search strategy using a protein
profile in conjunction with a six-frame translation of the same DNA sequence:
6ft - < R76849.seq | pfsearch -fy -C 5.0 sh3.prf -
EXIT CODE
On successful completion of its task, ptof 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.
SEE ALSO
pfscan(1), pfsearch(1), 2ft(1), 6ft(1)
AUTHOR
The pftools package was developed by Philipp Bucher.
Any comments or suggestions should be addressed to <pftools@sib.swiss>.
pftools 2.3 August 2003 PTOF(1)