compare-matrices -v 1 -format transfac -file $RSAT/public_html/tmp/wwwrun/2014/09/06/peak-motifs.2014-09-06.123915_2014-09-06.123915_sfIm4F/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/2014/09/06/peak-motifs.2014-09-06.123915_2014-09-06.123915_sfIm4F/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab Program version 1.118 Input files file2 $RSAT/public_html/tmp/wwwrun/2014/09/06/peak-motifs.2014-09-06.123915_2014-09-06.123915_sfIm4F/results/discovered_motifs/peak-motifs_motifs_discovered.tf file1 $RSAT/public_html/tmp/wwwrun/2014/09/06/peak-motifs.2014-09-06.123915_2014-09-06.123915_sfIm4F/results/discovered_motifs/peak-motifs_motifs_discovered.tf Output files alignments_1ton $RSAT/public_html/tmp/wwwrun/2014/09/06/peak-motifs.2014-09-06.123915_2014-09-06.123915_sfIm4F/results/discovered_motifs/peak-motifs_motifs_disco_compa_alignments_1ton.tab match_table_txt $RSAT/public_html/tmp/wwwrun/2014/09/06/peak-motifs.2014-09-06.123915_2014-09-06.123915_sfIm4F/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab html_index $RSAT/public_html/tmp/wwwrun/2014/09/06/peak-motifs.2014-09-06.123915_2014-09-06.123915_sfIm4F/results/discovered_motifs/peak-motifs_motifs_disco_compa_index.html alignments_1ton_html $RSAT/public_html/tmp/wwwrun/2014/09/06/peak-motifs.2014-09-06.123915_2014-09-06.123915_sfIm4F/results/discovered_motifs/peak-motifs_motifs_disco_compa_alignments_1ton.html match_table_html $RSAT/public_html/tmp/wwwrun/2014/09/06/peak-motifs.2014-09-06.123915_2014-09-06.123915_sfIm4F/results/discovered_motifs/peak-motifs_motifs_disco_compa.html prefix $RSAT/public_html/tmp/wwwrun/2014/09/06/peak-motifs.2014-09-06.123915_2014-09-06.123915_sfIm4F/results/discovered_motifs/peak-motifs_motifs_disco_compa Matrices file1 15 matrices $RSAT/public_html/tmp/wwwrun/2014/09/06/peak-motifs.2014-09-06.123915_2014-09-06.123915_sfIm4F/results/discovered_motifs/peak-motifs_motifs_discovered.tf file1 1 24 2 CrCCCTrsCCTGrCCyGGGkCACr file1 2 23 1 ATCCAAAGTCCAGAGCAGGGAAT file1 3 11 1513 mdGGGTCAGrr file1 4 24 1 GGCAGGGCAGCCGGGTCAGCCCTG file1 5 12 715 cmAAGGTCAGrr file1 6 24 2 TykGGCCAGyCCAAAGTCCArGAy file1 7 24 1 CACCTGCCCTTTGACCTGGCCACG file1 8 24 3 hdsGCmCmGGrCAkssyCAkGCCb file1 9 24 2 TmGGkCCAGkCCAAAGwCCAArwk file1 10 24 3 sdCCCAGCCAGrmCAkGGCwGGvk file1 11 21 18 ymAAGTCCAAAGTCCAGGGrw ... 5 more matrices file2 15 matrices $RSAT/public_html/tmp/wwwrun/2014/09/06/peak-motifs.2014-09-06.123915_2014-09-06.123915_sfIm4F/results/discovered_motifs/peak-motifs_motifs_discovered.tf file2 1 24 2 CrCCCTrsCCTGrCCyGGGkCACr file2 2 23 1 ATCCAAAGTCCAGAGCAGGGAAT file2 3 11 1513 mdGGGTCAGrr file2 4 24 1 GGCAGGGCAGCCGGGTCAGCCCTG file2 5 12 715 cmAAGGTCAGrr file2 6 24 2 TykGGCCAGyCCAAAGTCCArGAy file2 7 24 1 CACCTGCCCTTTGACCTGGCCACG file2 8 24 3 hdsGCmCmGGrCAkssyCAkGCCb file2 9 24 2 TmGGkCCAGkCCAAAGwCCAArwk file2 10 24 3 sdCCCAGCCAGrmCAkGGCwGGvk file2 11 21 18 ymAAGTCCAAAGTCCAGGGrw ... 5 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
oligos_7nt_test_vs_ctrl_m1 | oligos_7nt_test_vs_ctrl_m4 | oligos_7nt_test_vs_ctrl_m1 | oligos_7nt_test_vs_ctrl_m4 | 0.850 | 0.850 | 32.070 | 0.856 | 0.906 | 4.5000 | 0.93750 | 24 | 24 | 24 | 24 | 1.0000 | 1.0000 | 1.0000 | D | 0 | TykGGCCAGyCCAAAGTCCArGAy | TmGGkCCAGkCCAAAGwCCAArwk | 2 | 1 | 1 | 1 | 1 | 6 | 3 | 2.1429 | 1 |
oligos_6nt_test_vs_ctrl_m5 | oligos_8nt_test_vs_ctrl_m2 | oligos_6nt_test_vs_ctrl_m5 | oligos_8nt_test_vs_ctrl_m2 | 0.897 | 0.468 | 14.223 | 0.455 | 0.941 | 1.4080 | 0.93008 | 12 | 23 | 12 | 23 | 0.5217 | 1.0000 | 0.5217 | D | -11 | cmAAGGTCAGrr | ...........CAAAGGkCAGvh | 1 | 7 | 3 | 5 | 2 | 1 | 1 | 2.8571 | 2 |
oligos_8nt_test_vs_ctrl_m1 | oligos_8nt_test_vs_ctrl_m3 | oligos_8nt_test_vs_ctrl_m1 | oligos_8nt_test_vs_ctrl_m3 | 0.820 | 0.664 | 10.736 | 0.640 | 0.914 | 2.9086 | 0.92906 | 21 | 17 | 17 | 21 | 0.8095 | 0.8095 | 1.0000 | D | 4 | ....GTCCAAAGTCCAGGGrw | ksCCAGAGTCCAGGGwt | 3 | 5 | 5 | 3 | 3 | 3 | 2 | 3.4286 | 3 |
oligos_6nt_test_vs_ctrl_m3 | oligos_6nt_test_vs_ctrl_m5 | oligos_6nt_test_vs_ctrl_m3 | oligos_6nt_test_vs_ctrl_m5 | 0.767 | 0.703 | 11.593 | 0.705 | 0.878 | 2.6733 | 0.89490 | 11 | 12 | 11 | 12 | 0.9167 | 1.0000 | 0.9167 | D | -1 | mdGGGTCAGrr | .mAAGGTCAGrr | 7 | 3 | 4 | 2 | 7 | 2 | 6 | 4.4286 | 4 |
oligos_8nt_test_vs_ctrl_m1 | oligos_8nt_test_vs_ctrl_m4 | oligos_8nt_test_vs_ctrl_m1 | oligos_8nt_test_vs_ctrl_m4 | 0.779 | 0.741 | 2.169 | -0.105 | 0.897 | 4.1315 | 0.92814 | 21 | 20 | 20 | 21 | 0.9524 | 0.9524 | 1.0000 | R | 1 | .mAAGTCCAAAGTCCAGGGrw | VBAGGGCAAAGTCCAGGGRD | 5 | 2 | 6 | 6 | 4 | 5 | 5 | 4.7143 | 5 |
oligos_8nt_test_vs_ctrl_m3 | oligos_8nt_test_vs_ctrl_m4 | oligos_8nt_test_vs_ctrl_m3 | oligos_8nt_test_vs_ctrl_m4 | 0.782 | 0.665 | 1.415 | -0.138 | 0.897 | 3.4879 | 0.92232 | 17 | 20 | 17 | 20 | 0.8500 | 1.0000 | 0.8500 | R | -3 | ksCCAGAGTCCAGGGwt | ...GGGCAAAGTCCAGGGRD | 4 | 4 | 7 | 7 | 5 | 4 | 4 | 5.0000 | 6 |
oligos_6nt_test_vs_ctrl_m2 | oligos_8nt_test_vs_ctrl_m1 | oligos_6nt_test_vs_ctrl_m2 | oligos_8nt_test_vs_ctrl_m1 | 0.773 | 0.487 | 17.440 | 0.475 | 0.848 | 5.1605 | 0.90551 | 23 | 21 | 17 | 27 | 0.6296 | 0.7391 | 0.8095 | D | -4 | ATCCAAAGTCCAGAGCA...... | ....GTCCAAAGTCCAGGGrw | 6 | 6 | 2 | 4 | 6 | 7 | 7 | 5.4286 | 7 |
Host name rsat Job started 2014-09-06.124804 Job done 2014-09-06.124808 Seconds 2.25 user 2.25 system 0.05 cuser 1.97 ; csystem 0.11