| 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. |