matrix-quality result: Bacillus_subtilis Matrix FNR_bacillus.infogibbs
Command:
matrix-quality -v 2 -ms data/yeast_study_case/prodoric/FNR_bacillus/FNR_bacillus.infogibbs -matrix_format infogibbs -seq allup-noorf /Users/amedina/work_area/matrix_eval/data/sequences/allup/allup_noorf_Bacillus_subtilis.fas -perm allup-noorf 5 -roc_ref theor -img_format png,pdf -html_title ' Bacillus_subtilis Matrix FNR_bacillus.infogibbs ' -graph_option '-title1 FNR' -graph_option '-title2 FNR_bacillus.infogibbs' -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 FNR' -roc_option '-title2 FNR_bacillus.infogibbs ' -2str -pseudo 1 -bgfile /Users/amedina/local/rsa-tools/data/genomes/Bacillus_subtilis/oligo-frequencies/2nt_upstream-noorf_Bacillus_subtilis-ovlp-2str.freq.gz -th_prior /Users/amedina/local/rsa-tools/data/genomes/Bacillus_subtilis/oligo-frequencies/2nt_upstream-noorf_Bacillus_subtilis-ovlp-2str.freq.gz -o /Users/amedina/work_area/matrix_eval/results/Eukarya/matrix_quality20100324/FNR/FNR_bacillus.infogibbs
Figures
Matrix logo
Complementary cumulative distributions
Complementary cumulative distributions (logarithmic Y axis)
ROC curve (logarithmic X axis)
Matrix information
; convert-matrix -v 1 -i data/yeast_study_case/prodoric/FNR_bacillus/FNR_bacillus.infogibbs -from infogibbs -to tab -o /Users/amedina/work_area/matrix_eval/results/Eukarya/matrix_quality20100324/FNR/FNR_bacillus.infogibbs_matrix_info.txt -bgfile /Users/amedina/local/rsa-tools/data/genomes/Bacillus_subtilis/oligo-frequencies/2nt_upstream-noorf_Bacillus_subtilis-ovlp-2str.freq.gz -bg_format oligos -return counts,frequencies,weights,info,parameters,sites,logo -logo_format png,pdf -logo_opt '-e -M -t FNR_bacillus ' -logo_file /Users/amedina/work_area/matrix_eval/results/Eukarya/matrix_quality20100324/FNR/FNR_bacillus.infogibbs_FNR_bacillus_logo
; Input files
; input data/yeast_study_case/prodoric/FNR_bacillus/FNR_bacillus.infogibbs
; prior /Users/amedina/local/rsa-tools/data/genomes/Bacillus_subtilis/oligo-frequencies/2nt_upstream-noorf_Bacillus_subtilis-ovlp-2str.freq.gz
; Input format infogibbs
; Output files
; output /Users/amedina/work_area/matrix_eval/results/Eukarya/matrix_quality20100324/FNR/FNR_bacillus.infogibbs_matrix_info.txt
; Output format tab
; pseudo-weight 1
; Background model
; Strand insensitive
; Background pseudo-frequency 0.01
; Residue probabilities
; a 0.32071
; c 0.17947
; g 0.17897
; t 0.32085
a | 1 0 0 0 7 5 5 0 5 1 2 0 0 7 0 6
c | 0 0 0 0 0 1 0 1 0 3 0 0 7 0 7 0
g | 0 7 0 7 0 0 2 0 1 1 0 1 0 0 0 0
t | 6 0 7 0 0 1 0 6 1 2 5 6 0 0 0 1
//
a | 0.2 0.0 0.0 0.0 0.9 0.7 0.7 0.0 0.7 0.2 0.3 0.0 0.0 0.9 0.0 0.8
c | 0.0 0.0 0.0 0.0 0.0 0.1 0.0 0.1 0.0 0.4 0.0 0.0 0.9 0.0 0.9 0.0
g | 0.0 0.9 0.0 0.9 0.0 0.0 0.3 0.0 0.1 0.1 0.0 0.1 0.0 0.0 0.0 0.0
t | 0.8 0.0 0.9 0.0 0.0 0.2 0.0 0.8 0.2 0.3 0.7 0.8 0.0 0.0 0.0 0.2
//
a | -0.7 -2.1 -2.1 -2.1 1.0 0.7 0.7 -2.1 0.7 -0.7 -0.1 -2.1 -2.1 1.0 -2.1 0.9
c | -2.1 -2.1 -2.1 -2.1 -2.1 -0.2 -2.1 -0.2 -2.1 0.8 -2.1 -2.1 1.6 -2.1 1.6 -2.1
g | -2.1 1.6 -2.1 1.6 -2.1 -2.1 0.4 -2.1 -0.2 -0.2 -2.1 -0.2 -2.1 -2.1 -2.1 -2.1
t | 0.9 -2.1 1.0 -2.1 -2.1 -0.7 -2.1 0.9 -0.7 -0.1 0.7 0.9 -2.1 -2.1 -2.1 -0.7
//
a | -0.1 -0.1 -0.1 -0.1 1.0 0.5 0.5 -0.1 0.5 -0.1 -0.0 -0.1 -0.1 1.0 -0.1 0.7
c | -0.0 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0 0.3 -0.0 -0.0 1.4 -0.0 1.4 -0.0
g | -0.0 1.4 -0.0 1.4 -0.0 -0.0 0.1 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0
t | 0.7 -0.1 1.0 -0.1 -0.1 -0.1 -0.1 0.7 -0.1 -0.0 0.5 0.7 -0.1 -0.1 -0.1 -0.1
//
; Sites 7
>1
TGTGACATAGTTCACA
>2
TGTGAAATACATCACT
>3
TGTGATGTAATTCACA
>4
TGTGAAATACTTCACA
>5
TGTGAAGTGTTGCACA
>6
TGTGAAATACTTCACA
>7
AGTGAAACTTATCACA
;
; Matrix parameters
; Columns 16
; Rows 4
; Alphabet a|c|g|t
; Prior a:0.320705545565842|c:0.179472076806283|g:0.178972760582602|t:0.320849617045273
; program infogibbs
; matrix.nb 1
; sites 7
; pseudo 1
; info.log.base 2.71828
; min.prior 0.178973
; alphabet.size 4
; max.bits 2
; total.information 10.9832
; information.per.column 0.686453
; max.possible.info.per.col 1.72052
; consensus.strict tGTGAaatacttCACa
; consensus.strict.rc TGTGAAGTATTTCACA
; consensus.IUPAC tGTGAartacttCACa
; consensus.IUPAC.rc TGTGAAGTAYTTCACA
; consensus.regexp tGTGAa[ag]tacttCACa
; consensus.regexp.rc TGTGAAGTA[CT]TTCACA
; residues.content.crude.freq a:0.3482|c:0.1696|g:0.1696|t:0.3125
; G+C.content.crude.freq 0.339286
; residues.content.corrected.freq a:0.3448|c:0.1709|g:0.1708|t:0.3135
; G+C.content.corrected.freq 0.341681
; min(P(S|M)) 2.62977e-26
; max(P(S|M)) 0.0150617
; proba_range 0.0150617
; Wmin -32
; Wmax 17
; Wrange 49
; logo file:/Users/amedina/work_area/matrix_eval/results/Eukarya/matrix_quality20100324/FNR/FNR_bacillus.infogibbs_FNR_bacillus_logo_m1.png
; logo file:/Users/amedina/work_area/matrix_eval/results/Eukarya/matrix_quality20100324/FNR/FNR_bacillus.infogibbs_FNR_bacillus_logo_m1.pdf
; logo file:/Users/amedina/work_area/matrix_eval/results/Eukarya/matrix_quality20100324/FNR/FNR_bacillus.infogibbs_FNR_bacillus_logo_m1_rc.png
; logo file:/Users/amedina/work_area/matrix_eval/results/Eukarya/matrix_quality20100324/FNR/FNR_bacillus.infogibbs_FNR_bacillus_logo_m1_rc.pdf
; Job started 2010_03_26.124243
; Job done 2010_03_26.124255
Result files