; compare-matrices -v 1 -format transfac -file $RSAT/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -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/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab ; Program version 1.115 ; Input files ; file2 /home/rsat/rsa-tools/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/peak-motifs_motifs_discovered.tf ; file1 /home/rsat/rsa-tools/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/peak-motifs_motifs_discovered.tf ; Output files ; alignments_1ton /home/rsat/rsa-tools/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/peak-motifs_motifs_disco_compa_alignments_1ton.tab ; match_table_txt /home/rsat/rsa-tools/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab ; html_index /home/rsat/rsa-tools/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/peak-motifs_motifs_disco_compa_index.html ; alignments_1ton_html /home/rsat/rsa-tools/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/peak-motifs_motifs_disco_compa_alignments_1ton.html ; output_prefix /home/rsat/rsa-tools/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/peak-motifs_motifs_disco_compa ; match_table_html /home/rsat/rsa-tools/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/peak-motifs_motifs_disco_compa.html ; Matrices ; file1 9 matrices /home/rsat/rsa-tools/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/peak-motifs_motifs_discovered.tf ; file2 9 matrices /home/rsat/rsa-tools/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/peak-motifs_motifs_discovered.tf ; Threshold values ; Parameter Lower Upper ; w 5 none ; offset_rank none 1 ; wr 0.3 none ; cor 0.75 none ; Ncor 0.4 none ; ncor 0.4 none ; 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 local_words_7nt_m1 local_words_7nt_m3 local_words_7nt_m1 local_words_7nt_m3 0.969 0.969 7.137 0.970 0.991 0.3817 0.97920 21 21 21 21 1.0000 1.0000 1.0000 D 0 wbwCATTTcchgkAAATGtat kdaCATTTyCmrgaAATGtmw 1 1 8 1 1 1 1 2.0000 1 local_words_7nt_m1 local_words_7nt_m2 local_words_7nt_m1 local_words_7nt_m2 0.963 0.963 6.461 0.954 0.989 0.4568 0.97724 21 21 21 21 1.0000 1.0000 1.0000 D 0 wbwCATTTcchgkAAATGtat awaCATTTcybgkaaATGtaw 4 2 9 2 2 4 2 3.5714 2 oligos_7nt_mkv4_m1 positions_7nt_m3 oligos_7nt_mkv4_m1 positions_7nt_m3 0.966 0.846 10.644 0.844 0.986 0.3896 0.96847 14 16 14 16 0.8750 1.0000 0.8750 D 0 srTTTCCwGGAAay srTTTCYwGGAArt.. 2 6 2 6 5 2 3 3.7143 3 oligos_7nt_mkv4_m1 oligos_7nt_mkv4_m3 oligos_7nt_mkv4_m1 oligos_7nt_mkv4_m3 0.947 0.879 11.578 0.881 0.977 0.6084 0.95757 14 13 13 14 0.9286 0.9286 1.0000 D 1 .rTTTCCwGGAAay ryTTCCmrGAAry 6 5 1 5 9 6 9 5.8571 4 positions_7nt_m1 positions_7nt_m2 positions_7nt_m1 positions_7nt_m2 0.941 0.941 8.066 0.934 0.982 0.7676 0.97050 21 21 21 21 1.0000 1.0000 1.0000 D 0 wsTsrTTTCCwGGAAatsAsa dsTsatTTCCcrGAAATsAsr 9 4 7 3 4 9 6 6.0000 5 local_words_7nt_m2 local_words_7nt_m3 local_words_7nt_m2 local_words_7nt_m3 0.942 0.942 5.912 0.929 0.983 0.6934 0.97196 21 21 21 21 1.0000 1.0000 1.0000 D 0 awaCATTTcybgkaaATGtaw kdaCATTTyCmrgaAATGtmw 8 3 14 4 3 8 5 6.4286 6 oligos_7nt_mkv4_m1 positions_7nt_m1 oligos_7nt_mkv4_m1 positions_7nt_m1 0.963 0.642 9.650 0.644 0.985 0.4212 0.96722 14 21 14 21 0.6667 1.0000 0.6667 D -3 srTTTCCwGGAAay ...srTTTCCwGGAAat.... 3 15 4 12 6 3 4 6.7143 7 local_words_7nt_m3 positions_7nt_m2 local_words_7nt_m3 positions_7nt_m2 0.842 0.842 6.437 0.812 0.952 2.0195 0.95215 21 21 21 21 1.0000 1.0000 1.0000 D 0 kdaCATTTyCmrgaAATGtmw dsTsatTTCCcrGAAATsAsr 14 7 10 7 11 14 14 11.0000 8 oligos_7nt_mkv4_m3 positions_7nt_m1 oligos_7nt_mkv4_m3 positions_7nt_m1 0.927 0.574 9.770 0.577 0.968 0.8193 0.95077 13 21 13 21 0.6190 1.0000 0.6190 D -4 ryTTCCmrGAAry ....rTTTCCwGGAAat.... 10 19 3 14 12 10 10 11.1429 9 oligos_7nt_mkv4_m3 positions_7nt_m3 oligos_7nt_mkv4_m3 positions_7nt_m3 0.956 0.777 5.037 0.262 0.980 0.5091 0.96119 13 16 13 16 0.8125 1.0000 0.8125 R -2 ryTTCCmrGAAry ..AYTTCCWRGAAAY. 5 10 22 22 8 5 7 11.2857 10 positions_7nt_m1 positions_7nt_m3 positions_7nt_m1 positions_7nt_m3 0.945 0.720 5.359 0.294 0.979 0.6620 0.96404 21 16 16 21 0.7619 0.7619 1.0000 R 2 ..TsrTTTCCwGGAAats... YSAYTTCCWRGAAAYS 7 13 20 21 7 7 8 11.8571 11 local_words_7nt_m1 positions_7nt_m2 local_words_7nt_m1 positions_7nt_m2 0.824 0.824 6.141 0.786 0.946 2.2708 0.94926 21 21 21 21 1.0000 1.0000 1.0000 R 0 wbwCATTTcchgkAAATGtat YSTSATTTCYGGGAAATSASH 15 8 11 8 13 16 15 12.2857 12 oligos_7nt_mkv4_m1 positions_7nt_m2 oligos_7nt_mkv4_m1 positions_7nt_m2 0.898 0.599 8.852 0.587 0.958 1.1781 0.94518 14 21 14 21 0.6667 1.0000 0.6667 D -3 srTTTCCwGGAAay ...satTTCCcrGAAAT.... 13 18 6 13 15 13 13 13.0000 13 oligos_7nt_mkv4_m3 positions_7nt_m2 oligos_7nt_mkv4_m3 positions_7nt_m2 0.907 0.561 9.364 0.549 0.959 1.0633 0.94391 13 21 13 21 0.6190 1.0000 0.6190 D -4 ryTTCCmrGAAry ....atTTCCcrGAAAT.... 12 20 5 16 16 11 12 13.1429 14 local_words_7nt_m1 positions_7nt_m1 local_words_7nt_m1 positions_7nt_m1 0.814 0.814 5.915 0.768 0.944 2.3409 0.94848 21 21 21 21 1.0000 1.0000 1.0000 R 0 wbwCATTTcchgkAAATGtat TSTSATTTCCWGGAAAYSASW 16 9 13 9 14 17 16 13.4286 15 positions_7nt_m2 positions_7nt_m3 positions_7nt_m2 positions_7nt_m3 0.913 0.696 3.888 0.201 0.967 1.0715 0.95425 21 16 16 21 0.7619 0.7619 1.0000 R 2 ..TsatTTCCcrGAAATs... YSAYTTCCWRGAAAYS 11 14 23 23 10 12 11 14.8571 16 local_words_7nt_m3 positions_7nt_m1 local_words_7nt_m3 positions_7nt_m1 0.774 0.774 5.740 0.734 0.933 2.8217 0.94344 21 21 21 21 1.0000 1.0000 1.0000 R 0 kdaCATTTyCmrgaAATGtmw TSTSATTTCCWGGAAAYSASW 21 11 17 10 17 23 17 16.5714 17 local_words_7nt_m1 positions_7nt_m3 local_words_7nt_m1 positions_7nt_m3 0.805 0.613 5.774 0.554 0.927 2.3452 0.93232 21 16 16 21 0.7619 0.7619 1.0000 D 3 ...CATTTcchgkAAATGt.. srTTTCYwGGAArtsr 18 16 16 15 19 18 19 17.2857 18 local_words_7nt_m1 oligos_7nt_mkv4_m1 local_words_7nt_m1 oligos_7nt_mkv4_m1 0.813 0.542 6.083 0.495 0.925 2.1078 0.92667 21 14 14 21 0.6667 0.6667 1.0000 D 3 ...CATTTcchgkAAAT.... srTTTCCwGGAAay 17 21 12 17 21 15 21 17.7143 19 local_words_7nt_m2 positions_7nt_m2 local_words_7nt_m2 positions_7nt_m2 0.758 0.758 5.275 0.702 0.928 3.0222 0.94146 21 21 21 21 1.0000 1.0000 1.0000 R 0 awaCATTTcybgkaaATGtaw YSTSATTTCYGGGAAATSASH 23 12 21 11 18 24 18 18.1429 20 local_words_7nt_m3 oligos_7nt_mkv4_m1 local_words_7nt_m3 oligos_7nt_mkv4_m1 0.785 0.524 5.874 0.471 0.914 2.3996 0.92176 21 14 14 21 0.6667 0.6667 1.0000 D 3 ...CATTTyCmrgaAAT.... srTTTCCwGGAAay 20 22 15 18 22 20 22 19.8571 21 local_words_7nt_m3 positions_7nt_m3 local_words_7nt_m3 positions_7nt_m3 0.797 0.607 3.470 0.166 0.925 2.3938 0.93162 21 16 16 21 0.7619 0.7619 1.0000 R 2 ..aCATTTyCmrgaAATG... YSAYTTCCWRGAAAYS 19 17 24 24 20 19 20 20.4286 22 local_words_7nt_m3 oligos_7nt_mkv4_m3 local_words_7nt_m3 oligos_7nt_mkv4_m3 0.770 0.477 5.615 0.420 0.904 2.4838 0.91428 21 13 13 21 0.6190 0.6190 1.0000 D 4 ....ATTTyCmrgaAAT.... ryTTCCmrGAAry 22 23 18 19 23 21 23 21.2857 23 local_words_7nt_m1 oligos_7nt_mkv4_m3 local_words_7nt_m1 oligos_7nt_mkv4_m3 0.755 0.467 5.502 0.418 0.898 2.6592 0.91130 21 13 13 21 0.6190 0.6190 1.0000 R 4 ....ATTTcchgkAAAT.... RYTTCYKGGAARY 24 24 19 20 24 22 24 22.4286 24 ; Host name rsat ; Job started 2013-01-11.111029 ; Job done 2013-01-11.111036 ; Seconds 0.99 ; user 0.99 ; system 0.09 ; cuser 5.83 ; csystem 0.3