Home  |  Contact


     gtop - convert a profile in GCG format into PROSITE format


     gtop      [  -ahls  ]  [ -E gap_extend ] [ -F rescale ] [ -G

               gap_open ] [ -O offset ] gcg_profile | - [ parame-

               ters ]


     gtop  converts  a  profile generated by the GCG program Pro-

     fileMake, or by a GCG compatible profile  construction  pro-

     gram,  into PROSITE format, and optionally rescales the pro-

     file.  The result is written to  the  standard  output.   On

     input,  gtop  divides  all weights of the profile by 100, as

     GCG programs do.  On output, profile scores  are  multiplied

     by  the  rescaling factor F and rounded to the nearest inte-

     ger.  If symmetric gap weighting mode  is  chosen,  the  gap

     opening  weights  are  divided  by  2  and  assigned  to the

     MI, MD, IM, and DM transition  scores.   If  asymmetric  gap

     weighting  mode  is chosen, the gap opening weights are left

     unchanged and assigned to the MI and  MD  transition  scores

     only.   If no argument is specified, the program attempts to

     read the GCG formatted profile from the standard input.



          Input GCG profile.  If the filename is  replaced  by  a

          '-', gtop will read the input profile from stdin.

     -a   Apply  asymmetric  gap weighting mode (see the descrip-

          tion section).

     -h   Display usage help text.

     -l   Remove output line length limit.  Individual  lines  of

          the  output  profile can exceed a length of 132 charac-

          ters, removing the  need  to  wrap  them  over  several


     -s   Apply  symmetric  gap weighting mode (default) (see the

          description section).

     -E gap_extend

          Gap extension penalty.

          Default: 0.05

     -F rescale

          Score rescaling factor.

          Default: 100

     -G gap_open

          Gap opening penalty.

          Default: 4.5

     -O offset

          Output score offset. This value is added to all profile

          match scores after multiplication by the rescaling fac-

          tor F.

          Default: 0



          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.

     E=#  Gap extension penalty.

          Use option -E instead.

     F=#  Output score rescaling factor.

          Use option -F instead.

     G=#  Gap opening penalty.

          Use option -G instead.

     O=#  Output score offset.

          Use option -O instead.


     (1)  gtop -G 1.0 -E 1.0 -F 50  sh3.gpr  |  pfsearch  -far  -

          sh3.seq | sort -nr

          First  converts  the GCG profile 'sh3.gpr' into PROSITE

          format, then searches  the  protein  library  'sh3.seq'

          with  the reformatted profile to generate a sorted list

          of optimal alignment scores.  The pfsearch(1) option -r

          causes  alignment  scores  to be expressed in raw score

          units.  'sh3.seq'  contains  20  SH3  domain-containing

          protein sequences from SWISS-PROT release 32.


     On  successful  completion  of its task, gtop 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.


     gtop defines SCORE=0; N_SCORE=0; for the  mandatory  cut-off

     level  zero. These parameters should be changed to more rea-

     sonable values using a text editor, prior to profile  search



     pfsearch(1), pfscan(1), pfmake(1), sort(1)


     The pftools package was developped by Philipp Bucher.

     Any   comments   or   suggestions  should  be  addressed  to