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)

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)

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

Bairoch, A., Bucher P. (1994) PROSITE: recent developments. Nucleic Acids Research, Vol 22, No.17 3583-3589.
Bairoch, A., (1992) PROSITE: a dictionary of sites and patterns in proteins. Nucleic Acids Research, Vol 20, Supplement, 2013-2018.
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

Program name	Description
embossdata	Finds or fetches the data files read in by the EMBOSS programs
helixturnhelix	Report nucleic acid binding motifs
patmatdb	Search a protein sequence with a motif
patmatmotifs	Search a PROSITE motif database with a protein sequence
printsextract	Extract data from PRINTS
pscan	Scans proteins using PRINTS
rebaseextract	Extract data from REBASE
tfextract	Extract data from TRANSFAC
tfscan	Scans DNA sequences for transcription factors

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.