|   | prosextract | 
prosextract processes the PROSITE motif database for use by patmatmotifs. It reads the prosite.dat and prosite.doc files (from the Prosite distribution) from the specified directory and writes an output file (by default called prosite.lines) with the following information (corresponding lines from prosite.dat given in parentheses): i. Identity (ID). ii. Accession number (AC). iii. Motif pattern (PA). iv. The motif pattern converted a regular expression. Additionally, one output file per accession number is written containing documentation from prosite.doc.
| % prosextract Processes 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.
| 
   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 first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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) | |||
This directory contains output files.
This program most be run as a prerequisite to using patmatmotifs.
| Program name | Description | 
|---|---|
| aaindexextract | Extract amino acid property data from AAINDEX | 
| cutgextract | Extract codon usage tables from from CUTG database | 
| jaspextract | Extract data from JASPAR | 
| printsextract | Extract data from PRINTS database for use by pscan | 
| rebaseextract | Process the REBASE database for use by restriction enzyme applications | 
| tfextract | Process TRANSFAC transcription factor database for use by tfscan |