matrix-quality result: Rob_1d5y_AB
Command:
matrix-quality -v 1 -m /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/Rob/Rob_1d5y_AB.tab -matrix_format tab -seq db_sites /export/internal_use2/amedina/matrix_eval/data/Sites_FNA_R/Rob.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 Rob' -graph_option '-title2 /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/Rob/Rob_1d5y_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 Rob' -roc_option '-title2 /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/Rob/Rob_1d5y_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/Rob/Rob_1d5y_AB.tab/Rob_1d5y_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/Rob/Rob_1d5y_AB.tab -from tab -to tab -o /export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/Rob/Rob_1d5y_AB.tab/Rob_1d5y_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 Rob_1d5y_AB '
; Input files
; input /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/Rob/Rob_1d5y_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/Rob/Rob_1d5y_AB.tab/Rob_1d5y_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 | 14 34 6 0 74 14
c | 52 20 6 96 8 52
g | 16 22 78 0 7 14
t | 14 20 6 0 7 16
//
a | 0.1 0.4 0.1 0.0 0.8 0.1
c | 0.5 0.2 0.1 1.0 0.1 0.5
g | 0.2 0.2 0.8 0.0 0.1 0.1
t | 0.1 0.2 0.1 0.0 0.1 0.2
//
a | -0.7 0.2 -1.5 -4.6 1.0 -0.7
c | 1.0 0.0 -1.2 1.6 -0.9 1.0
g | -0.2 0.1 1.4 -4.6 -1.0 -0.3
t | -0.7 -0.4 -1.5 -4.6 -1.4 -0.6
//
a | -0.1 0.1 -0.1 -0.0 0.7 -0.1
c | 0.5 0.0 -0.1 1.6 -0.1 0.5
g | -0.0 0.0 1.1 -0.0 -0.1 -0.0
t | -0.1 -0.1 -0.1 -0.0 -0.1 -0.1
//
; Sites
;
; Matrix parameters
; Columns 6
; 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 3.40323
; information.per.column 0.567204
; max.possible.info.per.col 1.5879
; consensus.strict caGCac
; consensus.strict.rc GTGCTG
; consensus.IUPAC cvGCac
; consensus.IUPAC.rc GTGCBG
; consensus.regexp c[acg]GCac
; consensus.regexp.rc GTGC[CGT]G
; residues.content.crude.freq a:0.2465|c:0.4062|g:0.2378|t:0.1094
; G+C.content.crude.freq 0.644097
; residues.content.corrected.freq a:0.2470|c:0.4042|g:0.2375|t:0.1113
; G+C.content.corrected.freq 0.641702
; min(P(S|M)) 4.50043e-08
; max(P(S|M)) 0.0627177
; proba_range 0.0627177
; Wmin -9.3
; Wmax 6.1
; Wrange 15.4
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/Rob/Rob_1d5y_AB.tab/Rob_1d5y_AB_m1_logo.png
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/Rob/Rob_1d5y_AB.tab/Rob_1d5y_AB_m1_logo.pdf
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/Rob/Rob_1d5y_AB.tab/Rob_1d5y_AB_m1_logo_rc.png
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/Rob/Rob_1d5y_AB.tab/Rob_1d5y_AB_m1_logo_rc.pdf
; Job started 2010_03_11.202959
; Job done 2010_03_11.203003
Result files