matrix-quality result: MarA_1b10_A
Command:
matrix-quality -v 1 -m /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/MarA/MarA_1b10_A.tab -matrix_format tab -seq db_sites /export/internal_use2/amedina/matrix_eval/data/Sites_FNA_R/MarA.fna -perm db_sites 0 -scanopt db_sites '-uth rank_pm 1' -seq allup-noorf /export/internal_use2/amedina/matrix_eval/data/sequences/allup/Escherichia_coli_K12_allup-noorf_min30_max500.fasta -perm allup-noorf 1 -roc_ref theor -img_format png,pdf -graph_option '-title1 MarA' -graph_option '-title2 /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/MarA/MarA_1b10_A.tab' -graph_option '-xgstep1 5 -xgstep2 1' -graph_option '-ymin 1.0e-7 -ymax 1' -graph_option '-xmin -50 -xmax 30' -roc_option '-gstep1 0.1 -gstep2 0.05' -roc_option '-title1 MarA' -roc_option '-title2 /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/MarA/MarA_1b10_A.tab' -2str -pseudo 1 -bgfile /export/space2/rsa-tools/data/genomes/Escherichia_coli_K12/oligo-frequencies/1nt_upstream-noorf_Escherichia_coli_K12-ovlp-1str.freq -th_prior /export/space2/rsa-tools/data/genomes/Escherichia_coli_K12/oligo-frequencies/1nt_upstream-noorf_Escherichia_coli_K12-ovlp-1str.freq -o /export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/MarA/MarA_1b10_A.tab/MarA_1b10_A.tab_quality -graph_option '-colors /export/internal_use2/amedina/matrix_eval/data/quality_colors.tab ' -roc_option '-colors /export/internal_use2/amedina/matrix_eval/data/quality_colors.tab'
Figures
Matrix logo
Complementary cumulative distributions
Complementary cumulative distributions (logarithmic Y axis)
ROC curve (logarithmic X axis)
Matrix information
; convert-matrix -v 1 -i /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/MarA/MarA_1b10_A.tab -from tab -to tab -o /export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/MarA/MarA_1b10_A.tab/MarA_1b10_A.tab_quality_matrix_info.txt -bgfile /export/space2/rsa-tools/data/genomes/Escherichia_coli_K12/oligo-frequencies/1nt_upstream-noorf_Escherichia_coli_K12-ovlp-1str.freq -bg_format oligos -return counts,frequencies,weights,info,parameters,sites,logo -logo_format png,pdf -logo_opt '-e -M -t MarA_1b10_A '
; Input files
; input /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/MarA/MarA_1b10_A.tab
; prior /export/space2/rsa-tools/data/genomes/Escherichia_coli_K12/oligo-frequencies/1nt_upstream-noorf_Escherichia_coli_K12-ovlp-1str.freq
; Input format tab
; Output files
; output /export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/MarA/MarA_1b10_A.tab/MarA_1b10_A.tab_quality_matrix_info.txt
; Output format tab
; pseudo-weight 1
; Background model
; Bernoulli model (order=0)
; Strand sensitive
; Background pseudo-frequency 0.01
; Residue probabilities
; a 0.29107
; c 0.20737
; g 0.20436
; t 0.29721
a | 0 0 0 64 12 24 24 24 24 10 0 0 24 96 96
c | 0 96 96 10 64 24 24 24 24 0 0 96 24 0 0
g | 96 0 0 12 10 24 24 24 24 12 96 0 24 0 0
t | 0 0 0 10 10 24 24 24 24 74 0 0 24 0 0
//
a | 0.0 0.0 0.0 0.7 0.1 0.3 0.3 0.3 0.3 0.1 0.0 0.0 0.3 1.0 1.0
c | 0.0 1.0 1.0 0.1 0.7 0.2 0.2 0.2 0.2 0.0 0.0 1.0 0.2 0.0 0.0
g | 1.0 0.0 0.0 0.1 0.1 0.2 0.2 0.2 0.2 0.1 1.0 0.0 0.2 0.0 0.0
t | 0.0 0.0 0.0 0.1 0.1 0.3 0.3 0.3 0.3 0.8 0.0 0.0 0.3 0.0 0.0
//
a | -4.6 -4.6 -4.6 0.8 -0.8 -0.2 -0.2 -0.2 -0.2 -1.0 -4.6 -4.6 -0.2 1.2 1.2
c | -4.6 1.6 1.6 -0.7 1.2 0.2 0.2 0.2 0.2 -4.6 -4.6 1.6 0.2 -4.6 -4.6
g | 1.6 -4.6 -4.6 -0.5 -0.7 0.2 0.2 0.2 0.2 -0.5 1.6 -4.6 0.2 -4.6 -4.6
t | -4.6 -4.6 -4.6 -1.0 -1.0 -0.2 -0.2 -0.2 -0.2 0.9 -4.6 -4.6 -0.2 -4.6 -4.6
//
a | -0.0 -0.0 -0.0 0.5 -0.1 -0.0 -0.0 -0.0 -0.0 -0.1 -0.0 -0.0 -0.0 1.2 1.2
c | -0.0 1.6 1.6 -0.1 0.8 0.0 0.0 0.0 0.0 -0.0 -0.0 1.6 0.0 -0.0 -0.0
g | 1.6 -0.0 -0.0 -0.1 -0.1 0.0 0.0 0.0 0.0 -0.1 1.6 -0.0 0.0 -0.0 -0.0
t | -0.0 -0.0 -0.0 -0.1 -0.1 -0.0 -0.0 -0.0 -0.0 0.7 -0.0 -0.0 -0.0 -0.0 -0.0
//
; Sites
;
; Matrix parameters
; Columns 15
; Rows 4
; Alphabet a|c|g|t
; Prior a:0.291066898814656|c:0.207372933914605|g:0.204355073413807|t:0.297205093856932
; program tab
; matrix.nb 1
; pseudo 1
; info.log.base 2.71828
; min.prior 0.204355
; alphabet.size 4
; max.bits 2
; total.information 11.3843
; information.per.column 0.758955
; max.possible.info.per.col 1.5879
; consensus.strict GCCaCggggtGCgAA
; consensus.strict.rc TTCGCACCCCGTGGC
; consensus.IUPAC GCCaCsssstGCsAA
; consensus.IUPAC.rc TTSGCASSSSGTGGC
; consensus.regexp GCCaC[cg][cg][cg][cg]tGC[cg]AA
; consensus.regexp.rc TT[CG]GCA[CG][CG][CG][CG]GTGGC
; residues.content.crude.freq a:0.2764|c:0.3347|g:0.2403|t:0.1486
; G+C.content.crude.freq 0.575
; residues.content.corrected.freq a:0.2765|c:0.3334|g:0.2399|t:0.1501
; G+C.content.corrected.freq 0.573317
; min(P(S|M)) 4.34285e-27
; max(P(S|M)) 0.000313401
; proba_range 0.000313401
; Wmin -39.6
; Wmax 14.3
; Wrange 53.9
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/MarA/MarA_1b10_A.tab/MarA_1b10_A_m1_logo.png
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/MarA/MarA_1b10_A.tab/MarA_1b10_A_m1_logo.pdf
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/MarA/MarA_1b10_A.tab/MarA_1b10_A_m1_logo_rc.png
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/MarA/MarA_1b10_A.tab/MarA_1b10_A_m1_logo_rc.pdf
; Job started 2010_03_11.191418
; Job done 2010_03_11.191429
Result files