> # 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.