
                                prosextract 



Function

   Builds the PROSITE motif database for patmatmotifs to search

Description

   Takes the IDentity, ACcession number and motif PAttern line contents
   from prosite entries. Also converts the PAttern into a regular
   expression and writes these four pieces to an output file - defaulted
   to be called 'prosite.lines'.

Usage

   Here is a sample session with prosextract


% prosextract 
Builds the PROSITE motif database for patmatmotifs to search
Name of prosite directory [.]: 

   Go to the output files for this example

   The output files named after the prosite accession numbers can now
   also be seen in the prosite directory. This files are automatically
   created after prosextract is run.

Command line arguments

   Standard (Mandatory) qualifiers:
  [-infdat]            directory  Name of prosite directory

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers: (none)
   General qualifiers:
   -auto                boolean    Turn off prompts
   -stdout              boolean    Write standard output
   -filter              boolean    Read standard input, write standard output
   -options             boolean    Prompt for standard and additional values
   -debug               boolean    Write debug output to program.dbg
   -verbose             boolean    Report some/full command line options
   -help                boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning             boolean    Report warnings
   -error               boolean    Report errors
   -fatal               boolean    Report fatal errors
   -die                 boolean    Report deaths


                 Standard (Mandatory) qualifiers     Allowed values Default
   [-infdat]
   (Parameter 1) Name of prosite directory Directory
                 Additional (Optional) qualifiers    Allowed values Default
                 (none)
                 Advanced (Unprompted) qualifiers    Allowed values Default
                 (none)

Input file format

   These files must be the "prosite.dat" and "prosite.doc" file of a
   Prosite distribution, containing all current prosite data.

Output file format

   These files are held in the prosite subdirectory of the emboss data
   directory. The default names are "prosite.lines" and "PS*****"
   (accession number documentation files)

  Output files for usage example

  Directory: PROSITE

   This directory contains output files.

Data files

   See Input file format above.

Notes

   This program is most useful when used as a prerequisite for
   patmatmotifs.

References

    1. Bairoch, A., Bucher P. (1994) PROSITE: recent developments.
       Nucleic Acids Research, Vol 22, No.17 3583-3589.
    2. Bairoch, A., (1992) PROSITE: a dictionary of sites and patterns in
       proteins. Nucleic Acids Research, Vol 20, Supplement, 2013-2018.
    3. Peek, J., O'Reilly, T., Loukides, M., (1997) Unix Power Tools, 2nd
       Edition.

Warnings

   The program will warn the user if the input file is incorrectly
   formatted.

Diagnostic Error Messages

   As in warnings.

Exit status

   Always exits with status 0

Known bugs

See also

    Program name         Description
   aaindexextract Extract data from AAINDEX
   cutgextract    Extract data from CUTG
   printsextract  Extract data from PRINTS
   rebaseextract  Extract data from REBASE
   tfextract      Extract data from TRANSFAC

Author(s)

   Sinead O'Leary (current e-mail address unknown)
   while she was at:
   HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK

History

   Completed March 24 1999.

Target users

   This program is intended to be used by administrators responsible for
   software and database installation and maintenance.

Comments

   None
