##C Files: PSCM_to_PSEM.cpp TRAP.cpp PASTAA.cpp ##Calls: ./PSCM_to_PSEM TRANSFAC_MATRICES > ENERGY_MATRICES ./TRAP ENERGY_MATRICES FASTA_FILE > AFFINITIES ./PASTAA AFFINITIES GENE_LIST | sort -k2,2 -g > ENRICHMENT _______________________________________ ##Test example: SAMPLE_MATRIX est_liver_544 fullseq_200up_0down_TSS_Mm_genes.seq --> ./PSCM_to_PSEM SAMPLE_MATRIX > BRE_ENERGY ./TRAP BRE_ENERGY fullseq_200up_0down_TSS_Mm_genes.seq > BRE_AFFY ./PASTAA BRE_AFFY est_liver_544 | sort -k2,2 -g > BRE_LIVER_ENRICHMENT