****************************************************************************** Aging Research Computational Tools (ARCT) (0.9; January 31, 2005) ****************************************************************************** ARCT is a toolkit of Perl modules based on Bioperl, though some modules are independent of Bioperl. The aim of ARCT is to allow the comparative genomics of aging. ARCT is a collection of data-mining tools, algorithms, parsers, wrappers, spiders and web applications, etc. ****************************************************************************** SYSTEM REQUIREMENTS - Tested on Linux 2.4.x - Perl 5.8.0 - Bioperl 1.4 + Bioperl-run-1.4 + external modules (see Bioperl documentation) - TFBS 0.4.1 + PDL 2.4.0 (to use the TF module) - ClustalW 1.8.3 (to use the Clustal module) - Gibbs (to use the Gibbs module) - GD 2.06 (for graphical display of results) + associated files (i.e. libgd and libpng) INSTALL To install ARCT, just decompress and unpack the toolkit and change into the newly created directory (ARCT-xxx). Then build the module: perl Makefile.PL make And install: make install To use the ARCT toolkit: use ARCT::TF; ... THE JPM FILE FORMAT Frequently, ARCT uses a file format called JPM. JPM files usually have the .JPM extension. The JPM file format is as follows: # Accession number; Secondary accession (if any) Tab-delimited information: NAME: [text] ... The important thing to remember is that each number sign (#) marks the beginning of an entry. Information then follows a tab-delimited format. AUTHOR Joao Pedro de Magalhaes (http://jp.senescence.info/contact.php) ARCT website: http://genomics.senescence.info/software/ DOCUMENTATION It is highly advisable that you check main.pl for examples on how to use ARCT. main.pl also has a POD documentation. If you prefer to browse the modules, comments generally explain what each subroutine does and how it works. DISCLAIMER I am not responsible for any damage the use of ARCT may cause. Use at your own risk.