| ## EMBOSS: prosextract

# Program 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
    Extracting ID, AC & PA lines from the Prosite motif Database.
    Enter name of prosite directory: data/PROSITE

    % more prosite.lines
    ASN_GLYCOSYLATION PS00001
    N-glycosylation
    N-{P}-[ST]-{P}
    ^N[^P][ST][^P]

    CAMP_PHOSPHO_SITE PS00004
    cAMP-
    [RK](2)-x-[ST]
    ^[RK]{2}[^BJOUXZ][ST]

    PKC_PHOSPHO_SITE PS00005
    Protein
    [ST]-x-[RK]
    ^[ST][^BJOUXZ][RK]

    CK2_PHOSPHO_SITE PS00006
    Casein
    [ST]-x(2)-[DE]
    ^[ST][^BJOUXZ]{2}[DE]

    etc.......

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)
       General qualifiers:
      -help                bool       report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose

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
--- | ---
cutgextract | Extract data from CUTG
domainer | Build domain coordinate files
nrscope | Converts redundant EMBL-format SCOP file to non-redundant one
pdbtosp | Convert raw swissprot:pdb equivalence file to embl-like format
printsextract | Extract data from PRINTS
rebaseextract | Extract data from REBASE
scope | Convert raw scop classification file to embl-like format
scopparse | Reads raw scop classifications file and writes embl-like format scop classification file
seqnr | Converts redundant database results to a non-redundant set of hits
tfextract | Extract data from TRANSFAC

## Author(s)

This application was written by Sinead O'Leary (soleary@hgmp.mrc.ac.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