prosextract

Function

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

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


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

Author(s)

History

Target users

Comments