matrix-quality result: PutA_2rbf_AB
Command:
matrix-quality -v 1 -m /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/PutA/PutA_2rbf_AB.tab -matrix_format tab -seq db_sites /export/internal_use2/amedina/matrix_eval/data/Sites_FNA_R/PutA.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 PutA' -graph_option '-title2 /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/PutA/PutA_2rbf_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 PutA' -roc_option '-title2 /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/PutA/PutA_2rbf_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/PutA/PutA_2rbf_AB.tab/PutA_2rbf_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/PutA/PutA_2rbf_AB.tab -from tab -to tab -o /export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/PutA/PutA_2rbf_AB.tab/PutA_2rbf_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 PutA_2rbf_AB '
; Input files
; input /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/PutA/PutA_2rbf_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/PutA/PutA_2rbf_AB.tab/PutA_2rbf_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 24 14 7 51 96 0 0
c | 0 24 9 59 14 0 96 96
g | 96 24 51 14 17 0 0 0
t | 0 24 22 16 14 0 0 0
//
a | 0.0 0.3 0.1 0.1 0.5 1.0 0.0 0.0
c | 0.0 0.2 0.1 0.6 0.1 0.0 1.0 1.0
g | 1.0 0.2 0.5 0.1 0.2 0.0 0.0 0.0
t | 0.0 0.3 0.2 0.2 0.1 0.0 0.0 0.0
//
a | -4.6 -0.2 -0.7 -1.4 0.6 1.2 -4.6 -4.6
c | -4.6 0.2 -0.8 1.1 -0.3 -4.6 1.6 1.6
g | 1.6 0.2 0.9 -0.3 -0.1 -4.6 -4.6 -4.6
t | -4.6 -0.2 -0.3 -0.6 -0.7 -4.6 -4.6 -4.6
//
a | -0.0 -0.0 -0.1 -0.1 0.3 1.2 -0.0 -0.0
c | -0.0 0.0 -0.1 0.7 -0.1 -0.0 1.6 1.6
g | 1.6 0.0 0.5 -0.0 -0.0 -0.0 -0.0 -0.0
t | -0.0 -0.0 -0.1 -0.1 -0.1 -0.0 -0.0 -0.0
//
; 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 6.57515
; information.per.column 0.821893
; max.possible.info.per.col 1.5879
; consensus.strict GggCaACC
; consensus.strict.rc GGTTGCCC
; consensus.IUPAC GsgCaACC
; consensus.IUPAC.rc GGTTGCSC
; consensus.regexp G[cg]gCaACC
; consensus.regexp.rc GGTTGC[CG]C
; residues.content.crude.freq a:0.2500|c:0.3880|g:0.2630|t:0.0990
; G+C.content.crude.freq 0.651042
; residues.content.corrected.freq a:0.2504|c:0.3862|g:0.2624|t:0.1010
; G+C.content.corrected.freq 0.648575
; min(P(S|M)) 5.21277e-15
; max(P(S|M)) 0.0413337
; proba_range 0.0413337
; Wmin -21.4
; Wmax 8.9
; Wrange 30.3
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/PutA/PutA_2rbf_AB.tab/PutA_2rbf_AB_m1_logo.png
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/PutA/PutA_2rbf_AB.tab/PutA_2rbf_AB_m1_logo.pdf
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/PutA/PutA_2rbf_AB.tab/PutA_2rbf_AB_m1_logo_rc.png
; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/PutA/PutA_2rbf_AB.tab/PutA_2rbf_AB_m1_logo_rc.pdf
; Job started 2010_03_11.202051
; Job done 2010_03_11.202054
Result files