prosextract

 

Function

Build the PROSITE motif database for use by patmatmotifs

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 
Build the PROSITE motif database for use by patmatmotifs
PROSITE database 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:
  [-prositedir]        directory  PROSITE database 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 dying program messages

Standard (Mandatory) qualifiers Allowed values Default
[-prositedir]
(Parameter 1)		 PROSITE database 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 nameDescription
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