matrix-quality result: DnaA_1j1v_A
Command:
matrix-quality -v 1 -m /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/DnaA/DnaA_1j1v_A.tab -matrix_format tab -seq db_sites /export/internal_use2/amedina/matrix_eval/data/Sites_FNA_R/DnaA.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 DnaA' -graph_option '-title2 /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/DnaA/DnaA_1j1v_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 DnaA' -roc_option '-title2 /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/DnaA/DnaA_1j1v_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/DnaA/DnaA_1j1v_A.tab/DnaA_1j1v_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/DnaA/DnaA_1j1v_A.tab -from tab -to tab -o /export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/DnaA/DnaA_1j1v_A.tab/DnaA_1j1v_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 DnaA_1j1v_A '
; Input files
; input /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/DnaA/DnaA_1j1v_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/DnaA/DnaA_1j1v_A.tab/DnaA_1j1v_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 0 19 96 0 28
c | 0 0 0 0 11 0 19 9
g | 0 96 0 96 57 0 0 11
t | 96 0 96 0 9 0 77 48
//
a | 0.0 0.0 0.0 0.0 0.2 1.0 0.0 0.3
c | 0.0 0.0 0.0 0.0 0.1 0.0 0.2 0.1
g | 0.0 1.0 0.0 1.0 0.6 0.0 0.0 0.1
t | 1.0 0.0 1.0 0.0 0.1 0.0 0.8 0.5
//
a | -4.6 -4.6 -4.6 -4.6 -0.4 1.2 -4.6 0.0
c | -4.6 -4.6 -4.6 -4.6 -0.6 -4.6 -0.0 -0.8
g | -4.6 1.6 -4.6 1.6 1.1 -4.6 -4.6 -0.6
t | 1.2 -4.6 1.2 -4.6 -1.1 -4.6 1.0 0.5
//
a | -0.0 -0.0 -0.0 -0.0 -0.1 1.2 -0.0 0.0
c | -0.0 -0.0 -0.0 -0.0 -0.1 -0.0 -0.0 -0.1
g | -0.0 1.6 -0.0 1.6 0.6 -0.0 -0.0 -0.1
t | 1.2 -0.0 1.2 -0.0 -0.1 -0.0 0.8 0.3
//
; Sites
;
; Matrix parameters
; Columns 8
; 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 7.81527
; information.per.column 0.976908
; max.possible.info.per.col 1.5879
; consensus.strict TGTGGAtt
; consensus.strict.rc AATCCACA
; consensus.IUPAC TGTGGAtw
; consensus.IUPAC.rc WATCCACA
; consensus.regexp TGTGGAt[at]
; consensus.regexp.rc [AT]ATCCACA
; residues.content.crude.freq a:0.1862|c:0.0508|g:0.3385|t:0.4245
; G+C.content.crude.freq 0.389323
; residues.content.corrected.freq a:0.1873|c:0.0524|g:0.3372|t:0.4232
; G+C.content.corrected.freq 0.389554
; min(P(S|M)) 8.19144e-19
; max(P(S|M)) 0.225187
; proba_range 0.225187
; Wmin -29.5
; Wmax 9.5
; Wrange 39
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/DnaA/DnaA_1j1v_A.tab/DnaA_1j1v_A_m1_logo.png
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/DnaA/DnaA_1j1v_A.tab/DnaA_1j1v_A_m1_logo.pdf
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/DnaA/DnaA_1j1v_A.tab/DnaA_1j1v_A_m1_logo_rc.png
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/DnaA/DnaA_1j1v_A.tab/DnaA_1j1v_A_m1_logo_rc.pdf
; Job started 2010_03_11.181839
; Job done 2010_03_11.181843
Result files