; compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/footprintDB/footprintDB.motif.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_vs_db_footprintDB ; Program version 1.118 ; Input files ; file2 /vh/rsat/rsat/public_html/data/motif_databases/footprintDB/footprintDB.motif.tf ; file1 /vh/rsat/rsat/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4.tf ; Output files ; alignments_1ton /vh/rsat/rsat/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_vs_db_footprintDB_alignments_1ton.tab ; match_table_txt /vh/rsat/rsat/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_vs_db_footprintDB.tab ; html_index /vh/rsat/rsat/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_vs_db_footprintDB_index.html ; alignments_1ton_html /vh/rsat/rsat/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_vs_db_footprintDB_alignments_1ton.html ; match_table_html /vh/rsat/rsat/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_vs_db_footprintDB.html ; prefix /vh/rsat/rsat/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_vs_db_footprintDB ; Matrices ; file1 1 matrices /vh/rsat/rsat/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4.tf ; file1 1 11 37 ymTCCAGAccr ; file2 4196 matrices /vh/rsat/rsat/public_html/data/motif_databases/footprintDB/footprintDB.motif.tf ; file2 1 17 100 yyaymCATCAAwmwwmm ; file2 2 10 7 ACCGGAAGws ; file2 3 16 100 wwtksgTAATTACsdy ; file2 4 17 100 twrttaATTAwtaawwr ; file2 5 18 100 TCCGynnnnnnnnnCGGA ; file2 6 20 100 gwrastTTCCGGAAyrywrr ; file2 7 20 100 yrawygGyGCCGyrysackh ; file2 8 21 100 wmrmraAtmGAAGaaawawww ; file2 9 20 100 rkmkkakCACGTGmyyrvwy ; file2 10 6 1 CTATCA ; file2 11 18 66 hTTwCCwWAwwdGGhAat ; ... 4186 more matrices ; Column content ; 1 id1 Identifier of the first matrix ; 2 id2 Identifier of the second matrix ; 3 name1 Name of the first matrix ; 4 name2 Name of the second matrix ; 5 cor Pearson coefficient of correlation between frequency matrices ; 6 Ncor Normalized correlation. Ncor = cor * Wr ; 7 logoDP Dot product between the logo matrices. ; 8 NIcor Normalized Pearson correlation between the information content matrices. NIcor = Icor * Wr ; 9 NSW Normalized Sandelin-Wasserman similarity. NSW = SW/w ; 10 SSD sum of squared distance. ; 11 NsEucl relative Euclidian similarity. NsEucl = (max(dEucl) - dEucl)/max(dEucl) ; 12 w1 Width of the first matrix ; 13 w2 Width of the second matrix ; 14 w Alignment length (number of overlapping columns between matrix 1 and matrix 2, as a function of the offset) ; 15 W Total alignment length (overlapping + non-overlapping columns). W = w1 + w2 - w ; 16 Wr Relative alignment length (overlap divided by the total alignemnt length). Wr = w/W ; 17 wr1 Alignment length relative to the width of the first matrix. wr1 = w/w1 ; 18 wr2 Alignment length relative to the width of the second matrix. wr2 = w/w2 ; 19 strand "strand", i.e. orientation of matrix 2 relative to matrix 1 (D=direct; R=reverse) ; 20 offset shift of the second matrix relative to the first matrix (negative:left; positive: right) ; 21 consensus1 IUPAC consensus of matrix 1 (dots represent non-aligned columns) ; 22 consensus2 IUPAC consensus of matrix 2 (dots represent non-aligned columns) ; 23 rcor Matching rank for cor ; 24 rNcor Matching rank for Ncor ; 25 rlogoDP Matching rank for logoDP ; 26 rNIcor Matching rank for NIcor ; 27 rNsEucl Matching rank for NsEucl ; 28 rSSD Matching rank for SSD ; 29 rNSW Matching rank for NSW ; 30 rank_mean Mean of the matching ranks on all selected metrics ; 31 match_rank Rank of the match (sorting by rank_mean) #id1 id2 name1 name2 cor Ncor logoDP NIcor NSW SSD NsEucl w1 w2 w W Wr wr1 wr2 strand offset consensus1 consensus2 rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank dyads_m4 1921_PB0060.1_JASPAR_CORE_2009_ dyads_m4 1921_PB0060.1_JASPAR_CORE_2009_ 0.832 0.538 6.936 0.529 0.931 1.5076 0.92107 11 17 11 17 0.6471 1.0000 0.6471 D -2 ymTCCAGAccr ..watCCAGACrk.... 7 5 4 2 1 10 5 4.8571 1 dyads_m4 3697_UP00000_UniPROBE_20120919_ dyads_m4 3697_UP00000_UniPROBE_20120919_ 0.832 0.538 6.960 0.529 0.931 1.5090 0.92103 11 17 11 17 0.6471 1.0000 0.6471 D -2 ymTCCAGAccr ..wawCCAGACrk.... 8 6 3 1 2 11 6 5.2857 2 dyads_m4 2481_MA0092.1_JASPAR_CORE_2009_ dyads_m4 2481_MA0092.1_JASPAR_CORE_2009_ 0.846 0.769 3.725 0.338 0.932 1.3589 0.91757 11 10 10 11 0.9091 0.9091 1.0000 R 0 ymTCCAGAcc. AWKCCAGAYS 4 1 10 9 4 9 4 5.8571 3 dyads_m4 7423_HAND1_si_HOCOMOCO_v9_ dyads_m4 7423_HAND1_si_HOCOMOCO_v9_ 0.860 0.717 0.284 -0.134 0.938 1.2487 0.92098 11 11 10 12 0.8333 0.9091 0.9091 R -1 ymTCCAGAcc. .AWKCCAGAYV 3 2 15 15 3 6 3 6.7143 4 dyads_m4 1711_MA0152.1_JASPAR_CORE_2009_ dyads_m4 1711_MA0152.1_JASPAR_CORE_2009_ 0.840 0.420 5.947 0.398 0.913 1.0500 0.87924 11 7 6 12 0.5000 0.5455 0.8571 D -1 ymTCCA..... .TTTCCA 5 12 5 8 10 3 7 7.1429 5 dyads_m4 6130_1imh_C_3D-footprint_20130124_ dyads_m4 6130_1imh_C_3D-footprint_20130124_ 0.918 0.417 0.358 -0.024 0.952 0.4771 0.90232 11 5 5 11 0.4545 0.4545 1.0000 R 1 .mTCCA..... TTCCA 1 13 14 13 6 2 2 7.2857 6 dyads_m4 6074_1gji_A_3D-footprint_20130124_ dyads_m4 6074_1gji_A_3D-footprint_20130124_ 0.918 0.417 0.121 -0.063 0.952 0.4768 0.90235 11 5 5 11 0.4545 0.4545 1.0000 R 1 .mTCCA..... KTCCR 2 14 16 14 5 1 1 7.5714 7 dyads_m4 7686_UBIP1_f1_HOCOMOCO_v9_ dyads_m4 7686_UBIP1_f1_HOCOMOCO_v9_ 0.809 0.441 5.844 0.468 0.902 1.1757 0.87221 11 6 6 11 0.5455 0.5455 1.0000 D 4 ....CAGAcc. CAGArA 9 10 6 5 12 5 9 8.0000 8 dyads_m4 6322_1svc_P_3D-footprint_20130124_ dyads_m4 6322_1svc_P_3D-footprint_20130124_ 0.805 0.402 5.817 0.403 0.909 1.0924 0.87682 11 7 6 12 0.5000 0.5455 0.8571 D -1 ymTCCA..... .nnTCCc 10 16 7 7 11 4 8 9.0000 9 dyads_m4 7623_SMAD4_si_HOCOMOCO_v9_ dyads_m4 7623_SMAD4_si_HOCOMOCO_v9_ 0.801 0.582 4.026 0.195 0.894 1.7021 0.88469 11 8 8 11 0.7273 0.7273 1.0000 R 1 .mTCCAGAc.. RKMCAGAC 11 4 9 10 9 12 11 9.4286 10 dyads_m4 7622_SMAD3_f1_HOCOMOCO_v9_ dyads_m4 7622_SMAD3_f1_HOCOMOCO_v9_ 0.782 0.640 2.851 0.185 0.897 1.8482 0.89319 11 9 9 11 0.8182 0.8182 1.0000 R 1 .mTCCAGAcc. RGCCAGACA 12 3 11 11 8 13 10 9.7143 11 dyads_m4 2553_MA0292.1_JASPAR_CORE_2009_ dyads_m4 2553_MA0292.1_JASPAR_CORE_2009_ 0.765 0.487 6.968 0.500 0.862 1.9327 0.85957 11 7 7 11 0.6364 0.6364 1.0000 D 1 .mTCCAGA... hTCCGGA 14 7 2 3 15 14 15 10.0000 12 dyads_m4 2742_PF0055.1_JASPAR_CORE_2009_ dyads_m4 2742_PF0055.1_JASPAR_CORE_2009_ 0.836 0.456 1.961 0.003 0.887 1.3557 0.86278 11 6 6 11 0.5455 0.5455 1.0000 R 0 ymTCCA..... TTTCCA 6 9 12 12 14 8 14 10.7143 13 dyads_m4 2532_MA0266.1_JASPAR_CORE_2009_ dyads_m4 2532_MA0266.1_JASPAR_CORE_2009_ 0.757 0.482 7.967 0.486 0.850 2.0954 0.85378 11 7 7 11 0.6364 0.6364 1.0000 D 1 .mTCCAGA... sTCTAGA 16 8 1 4 16 15 16 10.8571 14 dyads_m4 2487_MA0098.1_JASPAR_CORE_2009_ dyads_m4 2487_MA0098.1_JASPAR_CORE_2009_ 0.761 0.415 5.191 0.426 0.887 1.3546 0.86284 11 6 6 11 0.5455 0.5455 1.0000 D 0 ymTCCA..... ywTCCk 15 15 8 6 13 7 13 11.0000 15 dyads_m4 2362_CN0199.1_JASPAR_CORE_2009_ dyads_m4 2362_CN0199.1_JASPAR_CORE_2009_ 0.775 0.431 0.369 -0.146 0.891 2.1725 0.89578 11 17 10 18 0.5556 0.9091 0.5882 R -7 ymTCCAGAcc. .......TTTCCAGAGC 13 11 13 16 7 16 12 12.5714 16 ; Host name biow ; Job started 2014-09-05.204103 ; Job done 2014-09-05.204137 ; Seconds 29.73 ; user 29.73 ; system 0.39 ; cuser 3.02 ; csystem 0.62