; matrix-from-patterns  -v 1 -sites -seq D2/regulonD2.rm.fna.peaks-rm/data/sequences/peaks_test.fasta -pl D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2.tab -bgfile D2/regulonD2.rm.fna.peaks-rm/results/composition/peaks_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 5 -max_asmb_width 20 -subst 1 -prefix oligos_5-7nt -flanks 2 -collect_method matrix-scan-quick -logo -cluster none -o D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm
; Input files
;	patterns	D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2.tab
;	sequence	D2/regulonD2.rm.fna.peaks-rm/data/sequences/peaks_test.fasta
; Output files
;	sig_matrices_split	D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_sig_matrices_split_matrix_list.tab
;	sig_matrices	D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_sig_matrices.tf
;	count_matrices	D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_count_matrices.txt
;	logo_basename	D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_count_matrices_logo
;	count_matrices_tf	D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_count_matrices.tf
;	gibbs_matrices	D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_gibbs_matrices.txt
;	sig_sites	D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_sig_sites.ft
;	err	D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_err.txt
;	output	D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm
;	log	D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_log.txt
;	assembly	D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm.asmb
;	links	D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_count_matrices_links.txt
; Number of patterns	76
; patterns -> assemblies
/var/www/html/rsat/perl-scripts/pattern-assembly -v 1 -i D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2.tab -2str -maxfl 1 -subst 1 -max_asmb_width 20 -toppat 100 -max_asmb_size 50 -max_asmb_width 20 -max_asmb_nb 5 -o D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm.asmb


/var/www/html/rsat/perl-scripts/pattern-assembly -v 1 -i D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2.tab -2str -maxfl 1 -subst 1 -max_asmb_width 20 -toppat 100 -max_asmb_size 50 -max_asmb_width 20 -max_asmb_nb 5 -o D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm.asmb
; Number of assemblies	5
; Number of assembled patterns	57
; assemblies -> significance matrices
/var/www/html/rsat/perl-scripts/convert-matrix -v 1 -i D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm.asmb -from assembly -to tf -return counts -decimals 2 -flanks 2 -top 5 -prefix oligos_5-7nt -o D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_sig_matrices.tf


/var/www/html/rsat/perl-scripts/convert-matrix -v 1 -i D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm.asmb -from assembly -to tf -return counts -decimals 2 -flanks 2 -top 5 -prefix oligos_5-7nt -o D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_sig_matrices.tf
; Rescaling significance matrices
/var/www/html/rsat/perl-scripts/convert-matrix -v 1 -i D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_sig_matrices.tf -from tf -to tf -return counts -decimals 3 -rescale 100 -o D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_sig_matrices_rescaled.tf


/var/www/html/rsat/perl-scripts/convert-matrix -v 1 -i D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_sig_matrices.tf -from tf -to tf -return counts -decimals 3 -rescale 100 -o D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_sig_matrices_rescaled.tf


/var/www/html/rsat/perl-scripts/convert-matrix -from tf -i D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_sig_matrices_rescaled.tf -to tab -split  -o D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_sig_matrices_split; rm -f D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_count_matrices.txt

; significance matrices + sequences -> sites
/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i D2/regulonD2.rm.fna.peaks-rm/data/sequences/peaks_test.fasta -m D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_sig_matrices_split_oligos_5-7nt_m1.tab -name oligos_5-7nt_m1 -2str -t 5 -return sites -bgfile D2/regulonD2.rm.fna.peaks-rm/results/composition/peaks_test_inclusive-1str-ovlp_2nt.txt >> D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_sig_sites.ft


/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i D2/regulonD2.rm.fna.peaks-rm/data/sequences/peaks_test.fasta -m D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_sig_matrices_split_oligos_5-7nt_m1.tab -name oligos_5-7nt_m1 -2str -t 5 -return sites -bgfile D2/regulonD2.rm.fna.peaks-rm/results/composition/peaks_test_inclusive-1str-ovlp_2nt.txt >> D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i D2/regulonD2.rm.fna.peaks-rm/data/sequences/peaks_test.fasta -m D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_sig_matrices_split_oligos_5-7nt_m2.tab -name oligos_5-7nt_m2 -2str -t 5 -return sites -bgfile D2/regulonD2.rm.fna.peaks-rm/results/composition/peaks_test_inclusive-1str-ovlp_2nt.txt >> D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_sig_sites.ft


/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i D2/regulonD2.rm.fna.peaks-rm/data/sequences/peaks_test.fasta -m D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_sig_matrices_split_oligos_5-7nt_m2.tab -name oligos_5-7nt_m2 -2str -t 5 -return sites -bgfile D2/regulonD2.rm.fna.peaks-rm/results/composition/peaks_test_inclusive-1str-ovlp_2nt.txt >> D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i D2/regulonD2.rm.fna.peaks-rm/data/sequences/peaks_test.fasta -m D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_sig_matrices_split_oligos_5-7nt_m3.tab -name oligos_5-7nt_m3 -2str -t 5 -return sites -bgfile D2/regulonD2.rm.fna.peaks-rm/results/composition/peaks_test_inclusive-1str-ovlp_2nt.txt >> D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_sig_sites.ft


/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i D2/regulonD2.rm.fna.peaks-rm/data/sequences/peaks_test.fasta -m D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_sig_matrices_split_oligos_5-7nt_m3.tab -name oligos_5-7nt_m3 -2str -t 5 -return sites -bgfile D2/regulonD2.rm.fna.peaks-rm/results/composition/peaks_test_inclusive-1str-ovlp_2nt.txt >> D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i D2/regulonD2.rm.fna.peaks-rm/data/sequences/peaks_test.fasta -m D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_sig_matrices_split_oligos_5-7nt_m4.tab -name oligos_5-7nt_m4 -2str -t 5 -return sites -bgfile D2/regulonD2.rm.fna.peaks-rm/results/composition/peaks_test_inclusive-1str-ovlp_2nt.txt >> D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_sig_sites.ft


/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i D2/regulonD2.rm.fna.peaks-rm/data/sequences/peaks_test.fasta -m D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_sig_matrices_split_oligos_5-7nt_m4.tab -name oligos_5-7nt_m4 -2str -t 5 -return sites -bgfile D2/regulonD2.rm.fna.peaks-rm/results/composition/peaks_test_inclusive-1str-ovlp_2nt.txt >> D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i D2/regulonD2.rm.fna.peaks-rm/data/sequences/peaks_test.fasta -m D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_sig_matrices_split_oligos_5-7nt_m5.tab -name oligos_5-7nt_m5 -2str -t 5 -return sites -bgfile D2/regulonD2.rm.fna.peaks-rm/results/composition/peaks_test_inclusive-1str-ovlp_2nt.txt >> D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_sig_sites.ft


/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i D2/regulonD2.rm.fna.peaks-rm/data/sequences/peaks_test.fasta -m D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_sig_matrices_split_oligos_5-7nt_m5.tab -name oligos_5-7nt_m5 -2str -t 5 -return sites -bgfile D2/regulonD2.rm.fna.peaks-rm/results/composition/peaks_test_inclusive-1str-ovlp_2nt.txt >> D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_sig_sites.ft
; sites -> transfac matrices
/var/www/html/rsat/perl-scripts/convert-matrix -v 0 -i D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_sig_sites.ft -from feature -to transfac -prefix oligos_5-7nt -return counts -return sites -o D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_count_matrices.tf


/var/www/html/rsat/perl-scripts/convert-matrix -v 0 -i D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_sig_sites.ft -from feature -to transfac -prefix oligos_5-7nt -return counts -return sites -o D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_count_matrices.tf
; transfac-formatted -> tab-formatted matrices
/var/www/html/rsat/perl-scripts/convert-matrix -v 1 -i D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_count_matrices.tf -from transfac -to tab -return counts -return sites -o D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_count_matrices.txt


/var/www/html/rsat/perl-scripts/convert-matrix -v 1 -i D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_count_matrices.tf -from transfac -to tab -return counts -return sites -o D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_count_matrices.txt
; sites -> count matrices
/var/www/html/rsat/perl-scripts/convert-matrix -v 1 -i D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_count_matrices.tf -from tf -to tab -return counts -return sites -return logo -logo_format png -logo_file D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_count_matrices_logo -o D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_count_matrices_links.txt


/var/www/html/rsat/perl-scripts/convert-matrix -v 1 -i D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_count_matrices.tf -from tf -to tab -return counts -return sites -return logo -logo_format png -logo_file D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_count_matrices_logo -o D2/regulonD2.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_count_matrices_links.txt
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