RSAT makefiles

This directory contains a series of makefiles, for the initialization, maintenance and testing of the Regulatory Sequence Analysis Tools (RSAT).

Installation and maintenance
init_rsat.mk Initialize of the tools for the first installation of RSAT, and import some genomes.
install_genomes.mk Parse and install new genomes from the NCBI genome repository. These genomes must previously be downloaded with downloads.mk
download.mk Download complete genomes and other data types (e.g. metabolic pathways) from NCBI and other databases (e.g. KEGG).
mirror.mk Maintenance of a RSAT mirror. Synchronization of different directories, principaly the genome data. This require the password of the main server.
server.mk Maintenance of the main RSAT server.
Program testing
check_disco_sig_distrib.mk Check the distibution of significance returned by string-based pattern discovery programs, by analyzing random sequences or random selections of promoters.
dyads_vs_oligos.mk Check the program dyad-analysis by comparing the statistics on dyads with spacing 0 with those calculated by oligo-anallysis on hexanucleotides.
Genome analysis
ortho_disco.mk Discover over-represented patterns (dyads) in upstream sequences of sets of orthologous genes.
Infer networks of co-regulated genes.
ortho_disco_validation.mk Validate the otho_disco.mk approach by analyzing all the genes in RegulonDB.
Miscellaneous
util.mk Utilities used by all the other makefile scripts.