Provided by: pftools_3.2.12-1_amd64 bug


       ptof - convert a protein profile into a frame-search profile


       ptof      [  -hlr ] [ -B init/term_score ] [ -F frameshift ] [ -I insert_multiplier ] [ -X
                 stop_codon ] [ -Y intron_open ] [ -Z intron_extend ] [ protein_profile | -  ]  [
                 parameters ]


       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.


              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

       -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)


       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.


       (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

              6ft - < R76849.seq | pfsearch -fy -C 5.0 sh3.prf -


       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.


       pfscan(1), pfsearch(1), 2ft(1), 6ft(1)


       The pftools package was developed by Philipp Bucher.
       Any comments or suggestions should be addressed to <>.