; 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/positions_7nt_m1/peak-motifs_positions_7nt_m1.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/positions_7nt_m1/peak-motifs_positions_7nt_m1_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/positions_7nt_m1/peak-motifs_positions_7nt_m1.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/positions_7nt_m1/peak-motifs_positions_7nt_m1_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/positions_7nt_m1/peak-motifs_positions_7nt_m1_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/positions_7nt_m1/peak-motifs_positions_7nt_m1_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/positions_7nt_m1/peak-motifs_positions_7nt_m1_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/positions_7nt_m1/peak-motifs_positions_7nt_m1_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/positions_7nt_m1/peak-motifs_positions_7nt_m1_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/positions_7nt_m1/peak-motifs_positions_7nt_m1.tf ; file1 1 11 6 vsAGGGGCCgg ; 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 positions_7nt_m1 2588_MA0342.1_JASPAR_CORE_2009_ positions_7nt_m1 2588_MA0342.1_JASPAR_CORE_2009_ 0.994 0.452 8.688 0.451 0.995 0.0524 0.96761 11 5 5 11 0.4545 0.4545 1.0000 D 2 ..AGGGG.... AGGGG 1 12 2 7 1 1 1 3.5714 1 positions_7nt_m1 2615_MA0381.1_JASPAR_CORE_2009_ positions_7nt_m1 2615_MA0381.1_JASPAR_CORE_2009_ 0.926 0.505 6.941 0.508 0.959 0.4973 0.91689 11 6 6 11 0.5455 0.5455 1.0000 D 5 .....GGCCgg GGCCrk 4 5 9 2 4 4 4 4.5714 2 positions_7nt_m1 2604_MA0366.1_JASPAR_CORE_2009_ positions_7nt_m1 2604_MA0366.1_JASPAR_CORE_2009_ 0.990 0.450 8.421 0.446 0.992 0.0794 0.96015 11 5 5 11 0.4545 0.4545 1.0000 D 2 ..AGGGG.... AGGGG 2 13 5 9 2 2 2 5.0000 3 positions_7nt_m1 2587_MA0341.1_JASPAR_CORE_2009_ positions_7nt_m1 2587_MA0341.1_JASPAR_CORE_2009_ 0.965 0.439 8.133 0.432 0.974 0.2647 0.92724 11 5 5 11 0.4545 0.4545 1.0000 D 2 ..AGGGG.... rGGGG 3 14 7 10 3 3 3 6.1429 4 positions_7nt_m1 2602_MA0364.1_JASPAR_CORE_2009_ positions_7nt_m1 2602_MA0364.1_JASPAR_CORE_2009_ 0.909 0.578 1.969 0.011 0.945 0.7670 0.91153 11 7 7 11 0.6364 0.6364 1.0000 R 0 vsAGGGG.... TCAGGGG 5 2 13 13 5 5 5 6.8571 5 positions_7nt_m1 1714_MA0155.1_JASPAR_CORE_2009_ positions_7nt_m1 1714_MA0155.1_JASPAR_CORE_2009_ 0.762 0.586 8.805 0.613 0.877 2.4653 0.88898 11 12 10 13 0.7692 0.9091 0.8333 D -2 vsAGGGGCCg. ..ymwGGGGkcr 14 1 1 1 6 15 11 7.0000 6 positions_7nt_m1 7480_KLF6_si_HOCOMOCO_v9_ positions_7nt_m1 7480_KLF6_si_HOCOMOCO_v9_ 0.785 0.499 5.483 0.493 0.882 1.6584 0.86991 11 7 7 11 0.6364 0.6364 1.0000 D 4 ....GGGCCgg GGGgCkG 10 6 11 3 11 7 8 8.0000 7 positions_7nt_m1 7492_MBD2_si_HOCOMOCO_v9_ positions_7nt_m1 7492_MBD2_si_HOCOMOCO_v9_ 0.829 0.414 6.288 0.375 0.901 1.3797 0.88135 11 10 7 14 0.5000 0.6364 0.7000 D 4 ....GGGCCgg sSkCCGG... 6 15 10 12 7 6 6 8.8571 8 positions_7nt_m1 2562_MA0306.1_JASPAR_CORE_2009_ positions_7nt_m1 2562_MA0306.1_JASPAR_CORE_2009_ 0.785 0.524 0.470 -0.128 0.884 1.8567 0.87956 11 9 8 12 0.6667 0.7273 0.8889 R -1 vsAGGGGC... .WWAGGGGW 9 4 14 14 8 9 7 9.2857 9 positions_7nt_m1 2711_PF0024.1_JASPAR_CORE_2009_ positions_7nt_m1 2711_PF0024.1_JASPAR_CORE_2009_ 0.798 0.466 7.679 0.428 0.878 1.7130 0.86779 11 8 7 12 0.5833 0.6364 0.8750 D -1 vsAGGGG.... .GGAGGrG 7 11 8 11 12 8 10 9.5714 10 positions_7nt_m1 7202_ATERF1_ArabidopsisPBM_20140210_ positions_7nt_m1 7202_ATERF1_ArabidopsisPBM_20140210_ 0.775 0.477 4.171 0.464 0.874 2.0084 0.87474 11 10 8 13 0.6154 0.7273 0.8000 D 3 ...GGGGCCgg GGcGsCGs.. 11 8 12 5 10 11 12 9.8571 11 positions_7nt_m1 2642_MA0423.1_JASPAR_CORE_2009_ positions_7nt_m1 2642_MA0423.1_JASPAR_CORE_2009_ 0.785 0.524 0.455 -0.144 0.880 1.9150 0.87768 11 9 8 12 0.6667 0.7273 0.8889 R -1 vsAGGGGC... .AWAGGGGK 8 3 15 15 9 10 9 9.8571 12 positions_7nt_m1 7268_TCP23_ArabidopsisPBM_20140210_ positions_7nt_m1 7268_TCP23_ArabidopsisPBM_20140210_ 0.771 0.474 8.646 0.452 0.856 2.2962 0.86606 11 10 8 13 0.6154 0.7273 0.8000 D 3 ...GGGGCCgg GGGGCCCA.. 12 9 4 6 13 13 13 10.0000 13 positions_7nt_m1 2693_PF0006.1_JASPAR_CORE_2009_ positions_7nt_m1 2693_PF0006.1_JASPAR_CORE_2009_ 0.761 0.484 8.413 0.478 0.842 2.2097 0.84984 11 7 7 11 0.6364 0.6364 1.0000 D 4 ....GGGCCgg GGGCGGG 15 7 6 4 15 12 15 10.5714 14 positions_7nt_m1 7266_TCP15_ArabidopsisPBM_20140210_ positions_7nt_m1 7266_TCP15_ArabidopsisPBM_20140210_ 0.768 0.473 8.667 0.447 0.855 2.3189 0.86540 11 10 8 13 0.6154 0.7273 0.8000 D 3 ...GGGGCCgg GGGGCCCA.. 13 10 3 8 14 14 14 10.8571 15 ; Host name biow ; Job started 2014-09-05.203226 ; Job done 2014-09-05.203301 ; Seconds 30.03 ; user 30.03 ; system 0.45 ; cuser 3.47 ; csystem 0.64