matrix-quality result: TrpR_1rcs_AB
Command:
matrix-quality -v 1 -m /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/TrpR/TrpR_1rcs_AB.tab -matrix_format tab -seq db_sites /export/internal_use2/amedina/matrix_eval/data/Sites_FNA_R/TrpR.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 TrpR' -graph_option '-title2 /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/TrpR/TrpR_1rcs_AB.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 TrpR' -roc_option '-title2 /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/TrpR/TrpR_1rcs_AB.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/TrpR/TrpR_1rcs_AB.tab/TrpR_1rcs_AB.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/TrpR/TrpR_1rcs_AB.tab -from tab -to tab -o /export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/TrpR/TrpR_1rcs_AB.tab/TrpR_1rcs_AB.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 TrpR_1rcs_AB '
; Input files
; input /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/TrpR/TrpR_1rcs_AB.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/TrpR/TrpR_1rcs_AB.tab/TrpR_1rcs_AB.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 86 0 24 96 4 24 24 24 24 14 7 52 0 0 96 0
c | 0 0 1 96 24 0 9 24 24 24 24 67 4 14 0 14 0 96
g | 96 0 9 0 24 0 72 24 24 24 24 9 4 11 96 0 0 0
t | 0 96 0 0 24 0 11 24 24 24 24 6 81 19 0 82 0 0
//
a | 0.0 0.0 0.9 0.0 0.3 1.0 0.0 0.3 0.3 0.3 0.3 0.1 0.1 0.5 0.0 0.0 1.0 0.0
c | 0.0 0.0 0.0 1.0 0.2 0.0 0.1 0.2 0.2 0.2 0.2 0.7 0.0 0.1 0.0 0.1 0.0 1.0
g | 1.0 0.0 0.1 0.0 0.2 0.0 0.7 0.2 0.2 0.2 0.2 0.1 0.0 0.1 1.0 0.0 0.0 0.0
t | 0.0 1.0 0.0 0.0 0.3 0.0 0.1 0.3 0.3 0.3 0.3 0.1 0.8 0.2 0.0 0.8 0.0 0.0
//
a | -4.6 -4.6 1.1 -4.6 -0.2 1.2 -1.9 -0.2 -0.2 -0.2 -0.2 -0.7 -1.4 0.6 -4.6 -4.6 1.2 -4.6
c | -4.6 -4.6 -2.8 1.6 0.2 -4.6 -0.8 0.2 0.2 0.2 0.2 1.2 -1.6 -0.3 -4.6 -0.3 -4.6 1.6
g | 1.6 -4.6 -0.8 -4.6 0.2 -4.6 1.3 0.2 0.2 0.2 0.2 -0.8 -1.6 -0.6 1.6 -4.6 -4.6 -4.6
t | -4.6 1.2 -4.6 -4.6 -0.2 -4.6 -0.9 -0.2 -0.2 -0.2 -0.2 -1.5 1.0 -0.4 -4.6 1.0 -4.6 -4.6
//
a | -0.0 -0.0 1.0 -0.0 -0.0 1.2 -0.1 -0.0 -0.0 -0.0 -0.0 -0.1 -0.1 0.3 -0.0 -0.0 1.2 -0.0
c | -0.0 -0.0 -0.0 1.6 0.0 -0.0 -0.1 0.0 0.0 0.0 0.0 0.8 -0.1 -0.1 -0.0 -0.1 -0.0 1.6
g | 1.6 -0.0 -0.1 -0.0 0.0 -0.0 1.0 0.0 0.0 0.0 0.0 -0.1 -0.1 -0.1 1.6 -0.0 -0.0 -0.0
t | -0.0 1.2 -0.0 -0.0 -0.0 -0.0 -0.1 -0.0 -0.0 -0.0 -0.0 -0.1 0.9 -0.1 -0.0 0.9 -0.0 -0.0
//
; Sites
;
; Matrix parameters
; Columns 18
; 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 13.4138
; information.per.column 0.745212
; max.possible.info.per.col 1.5879
; consensus.strict GTACgAGggggCTaGTAC
; consensus.strict.rc GTACTAGCCCCCTCGTAC
; consensus.IUPAC GTACsAGssssCTaGTAC
; consensus.IUPAC.rc GTACTAGSSSSCTSGTAC
; consensus.regexp GTAC[cg]AG[cg][cg][cg][cg]CTaGTAC
; consensus.regexp.rc GTACTAG[CG][CG][CG][CG]CT[CG]GTAC
; residues.content.crude.freq a:0.2749|c:0.2436|g:0.2413|t:0.2402
; G+C.content.crude.freq 0.484954
; residues.content.corrected.freq a:0.2751|c:0.2433|g:0.2409|t:0.2408
; G+C.content.corrected.freq 0.484199
; min(P(S|M)) 1.70313e-32
; max(P(S|M)) 0.000164179
; proba_range 0.000164179
; Wmin -47.7
; Wmax 17.3
; Wrange 65
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/TrpR/TrpR_1rcs_AB.tab/TrpR_1rcs_AB_m1_logo.png
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/TrpR/TrpR_1rcs_AB.tab/TrpR_1rcs_AB_m1_logo.pdf
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/TrpR/TrpR_1rcs_AB.tab/TrpR_1rcs_AB_m1_logo_rc.png
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/TrpR/TrpR_1rcs_AB.tab/TrpR_1rcs_AB_m1_logo_rc.pdf
; Job started 2010_03_11.203914
; Job done 2010_03_11.204012
Result files