matrix-quality result: PhoB_1gxp_AB
Command:
matrix-quality -v 1 -m /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/PhoB/PhoB_1gxp_AB.tab -matrix_format tab -seq db_sites /export/internal_use2/amedina/matrix_eval/data/Sites_FNA_R/PhoB.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 PhoB' -graph_option '-title2 /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/PhoB/PhoB_1gxp_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 PhoB' -roc_option '-title2 /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/PhoB/PhoB_1gxp_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/PhoB/PhoB_1gxp_AB.tab/PhoB_1gxp_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/PhoB/PhoB_1gxp_AB.tab -from tab -to tab -o /export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/PhoB/PhoB_1gxp_AB.tab/PhoB_1gxp_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 PhoB_1gxp_AB '
; Input files
; input /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/PhoB/PhoB_1gxp_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/PhoB/PhoB_1gxp_AB.tab/PhoB_1gxp_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 | 6 6 24 12 3 96 0 86 24 0 0 6 0 24 24 6 96 0 96
c | 81 76 24 12 3 0 96 3 24 96 0 6 0 24 24 6 0 96 0
g | 3 6 24 12 86 0 0 4 24 0 0 6 0 24 24 78 0 0 0
t | 6 8 24 60 4 0 0 3 24 0 96 78 96 24 24 6 0 0 0
//
a | 0.1 0.1 0.3 0.1 0.0 1.0 0.0 0.9 0.3 0.0 0.0 0.1 0.0 0.3 0.3 0.1 1.0 0.0 1.0
c | 0.8 0.8 0.2 0.1 0.0 0.0 1.0 0.0 0.2 1.0 0.0 0.1 0.0 0.2 0.2 0.1 0.0 1.0 0.0
g | 0.0 0.1 0.2 0.1 0.9 0.0 0.0 0.0 0.2 0.0 0.0 0.1 0.0 0.2 0.2 0.8 0.0 0.0 0.0
t | 0.1 0.1 0.3 0.6 0.0 0.0 0.0 0.0 0.3 0.0 1.0 0.8 1.0 0.3 0.3 0.1 0.0 0.0 0.0
//
a | -1.5 -1.5 -0.2 -0.8 -2.1 1.2 -4.6 1.1 -0.2 -4.6 -4.6 -1.5 -4.6 -0.2 -0.2 -1.5 1.2 -4.6 1.2
c | 1.4 1.3 0.2 -0.5 -1.8 -4.6 1.6 -1.8 0.2 1.6 -4.6 -1.2 -4.6 0.2 0.2 -1.2 -4.6 1.6 -4.6
g | -1.8 -1.2 0.2 -0.5 1.5 -4.6 -4.6 -1.6 0.2 -4.6 -4.6 -1.2 -4.6 0.2 0.2 1.4 -4.6 -4.6 -4.6
t | -1.5 -1.2 -0.2 0.7 -1.9 -4.6 -4.6 -2.2 -0.2 -4.6 1.2 1.0 1.2 -0.2 -0.2 -1.5 -4.6 -4.6 -4.6
//
a | -0.1 -0.1 -0.0 -0.1 -0.1 1.2 -0.0 1.0 -0.0 -0.0 -0.0 -0.1 -0.0 -0.0 -0.0 -0.1 1.2 -0.0 1.2
c | 1.2 1.0 0.0 -0.1 -0.1 -0.0 1.6 -0.1 0.0 1.6 -0.0 -0.1 -0.0 0.0 0.0 -0.1 -0.0 1.6 -0.0
g | -0.1 -0.1 0.0 -0.1 1.3 -0.0 -0.0 -0.1 0.0 -0.0 -0.0 -0.1 -0.0 0.0 0.0 1.1 -0.0 -0.0 -0.0
t | -0.1 -0.1 -0.0 0.5 -0.1 -0.0 -0.0 -0.1 -0.0 -0.0 1.2 0.8 1.2 -0.0 -0.0 -0.1 -0.0 -0.0 -0.0
//
; Sites
;
; Matrix parameters
; Columns 19
; 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 15.6736
; information.per.column 0.824926
; max.possible.info.per.col 1.5879
; consensus.strict CCgtGACAgCTtTggGACA
; consensus.strict.rc TGTCCCAAAGCTGTCACGG
; consensus.IUPAC CCstGACAsCTtTssGACA
; consensus.IUPAC.rc TGTCSSAAAGSTGTCASGG
; consensus.regexp CC[cg]tGACA[cg]CTtT[cg][cg]GACA
; consensus.regexp.rc TGTC[CG][CG]AAAG[CG]TGTCA[CG]GG
; residues.content.crude.freq a:0.2791|c:0.3130|g:0.1595|t:0.2484
; G+C.content.crude.freq 0.472588
; residues.content.corrected.freq a:0.2792|c:0.3120|g:0.1600|t:0.2489
; G+C.content.corrected.freq 0.47196
; min(P(S|M)) 1.78999e-33
; max(P(S|M)) 0.000778995
; proba_range 0.000778995
; Wmin -48.9
; Wmax 20.1
; Wrange 69
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/PhoB/PhoB_1gxp_AB.tab/PhoB_1gxp_AB_m1_logo.png
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/PhoB/PhoB_1gxp_AB.tab/PhoB_1gxp_AB_m1_logo.pdf
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/PhoB/PhoB_1gxp_AB.tab/PhoB_1gxp_AB_m1_logo_rc.png
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/PhoB/PhoB_1gxp_AB.tab/PhoB_1gxp_AB_m1_logo_rc.pdf
; Job started 2010_03_11.195605
; Job done 2010_03_11.195731
Result files