; footprint-discovery  -v 1 -nodie -org Escherichia_coli_GCF_000005845.2_ASM584v2 -taxon Gammaproteobacteria -genes $RSAT/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/lexA_genes -sep_genes -lth occ 1 -lth occ_sig 0 -uth rank 50 -return occ,proba,rank -filter -bg_model taxfreq -task query_seq,filter_dyads,orthologs,ortho_seq,purge,dyads,maps,gene_index,index -o $RSAT/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ
; Program version       	1.116
; Working directory     	/space23/rsat/public_html
; Computer name         	sinik
; Query organism        	Escherichia_coli_GCF_000005845.2_ASM584v2
; Reference taxon       	Gammaproteobacteria

; 2018-03-21.142509
$RSAT/perl-scripts/get-orthologs -nowarn -i $RSAT/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_query_genes.tab -org Escherichia_coli_GCF_000005845.2_ASM584v2 -taxon Gammaproteobacteria -return query_name,query_organism -return ident -uth rank 1 -lth ali_len 50 -uth e_value 1e-05 -return e_value -only_blast -o $RSAT/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_bbh.tab


; 2018-03-21.142932
$RSAT/perl-scripts/dyad-analysis -v 1  -return occ,proba,rank -expfreq $RSAT/public_html/data/taxon_frequencies/Gammaproteobacteria/dyads_3nt_sp0-20_upstream-noorf_Gammaproteobacteria-noov-2str.freq -accept $RSAT/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_filter_dyads.tab -lth occ 1 -lth occ_sig 0 -uth rank 50 -i $RSAT/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_seq_purged.fasta -l 3 -sp 0-20 -2str -noov -sort -o $RSAT/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0.tab


; 2018-03-21.142939
$RSAT/perl-scripts/text-to-html -i $RSAT/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0.tab -font variable -chunk 1000 -o $RSAT/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0.html


; 2018-03-21.142940
$RSAT/perl-scripts/pattern-assembly -v 1 -i $RSAT/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0.tab -subst 1 -weight 5 -maxfl 1 -toppat 50 -max_asmb_nb 5 -o $RSAT/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0.asmb


; 2018-03-21.142947
$RSAT/perl-scripts/matrix-from-patterns -v 1 -seq $RSAT/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_seq.fasta -asmb $RSAT/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0.asmb -prefix lexA -format fasta  -sites -uth Pval 0.00025 -bginput -markov 0 -flanks 2 -2str -logo -o $RSAT/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm


; 2018-03-21.143009
$RSAT/perl-scripts/dna-pattern -return limits,sites -origin -0 -N 4 -pl $RSAT/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0.tab -format fasta -i $RSAT/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_seq.fasta | $RSAT/perl-scripts/convert-features -from dnapat -to ft | $RSAT/perl-scripts/feature-map -title 'dyad map; Gammaproteobacteria; Escherichia_coli_GCF_000005845.2_ASM584v2; lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq' -format png -scalebar -legend -scorethick -mapthick 16 -mspacing 2 -mlen 600 -o $RSAT/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0.png


; 2018-03-21.143102
$RSAT/perl-scripts/matrix-scan -quick -return limits,sites,pval -decimals 1 -origin end -consensus_name -matrix_format transfac -m $RSAT/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm_count_matrices.tf -pseudo 1 -decimals 1 -2str -bg_pseudo 0.01 -lth score 1 -uth pval 1e-4 -n score -seq_format fasta -bginput -markov 1 -i $RSAT/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_seq.fasta | $RSAT/perl-scripts/feature-map -title 'Site map; Gammaproteobacteria; Escherichia_coli_GCF_000005845.2_ASM584v2; lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq' -format png -scalebar -legend -scorethick -mapthick 16 -mspacing 2 -mlen 600 -o $RSAT/public_html/tmp/apache/2018/03/21/footprint-discovery_Gammaproteobacteria_Escherichia_coli_GCF_000005845.2_ASM584v2_lexA_2018-03-21.142439_2018-03-21.142439_C9MNSJ/Gammaproteobacteria/Escherichia_coli_GCF_000005845.2_ASM584v2/lexA/lexA_Escherichia_coli_GCF_000005845.2_ASM584v2_Gammaproteobacteria_taxfreq_ortho_dyads_3nt_sp0-20-2str-noov_taxfreq_sig0_pssm.png

