Please help by correcting and extending the Wiki pages.
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|
|PROSITE database directory||Directory|
|Additional (Optional) qualifiers||Allowed values||Default|
|Advanced (Unprompted) qualifiers||Allowed values||Default|
This directory contains output files.
This program most be run as a prerequisite to using patmatmotifs.
|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|