| 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
    Enter name of prosite directory: ../../data/

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

       Mandatory qualifiers:
      [-infdat]            string     Enter name of prosite directory

       Optional qualifiers: (none)
       Advanced 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 required and optional values
       -debug               boolean    Write debug output to program.dbg
       -acdlog              boolean    Write ACD processing log to program.acdlog
       -acdpretty           boolean    Rewrite ACD file as program.acdpretty
       -acdtable            boolean    Write HTML table of options
       -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

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-infdat] (Parameter 1) | Enter name of prosite directory | Any string is accepted | An empty string is accepted
Optional qualifiers | Allowed values | Default
(none)
Advanced 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)

## 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