compare-matrices -v 1 -format transfac -file $RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/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/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab Program version 1.118 Input files file2 $RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_motifs/peak-motifs_motifs_discovered.tf file1 $RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_motifs/peak-motifs_motifs_discovered.tf Output files alignments_1ton $RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_motifs/peak-motifs_motifs_disco_compa_alignments_1ton.tab match_table_txt $RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab html_index $RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_motifs/peak-motifs_motifs_disco_compa_index.html alignments_1ton_html $RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_motifs/peak-motifs_motifs_disco_compa_alignments_1ton.html match_table_html $RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_motifs/peak-motifs_motifs_disco_compa.html prefix $RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_motifs/peak-motifs_motifs_disco_compa Matrices file1 17 matrices $RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_motifs/peak-motifs_motifs_discovered.tf file1 1 10 630 wwCTTTTCwh file1 2 10 792 wwAAATTAtw file1 3 12 1005 syCACTGCAmyc file1 4 13 849 ccAGGCTGGGCtc file1 5 11 1120 mkCCTCCCrms file1 6 10 6 CGCGCGCGCG file1 7 12 1277 dtATTTTTAdww file1 8 11 893 yyCTGCCTCmg file1 9 11 789 cyCTGTCTCwa file1 10 12 733 ccyCCACCTCss file1 11 12 730 wsaCTCTGTCtc ... 7 more matrices file2 17 matrices $RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_motifs/peak-motifs_motifs_discovered.tf file2 1 10 630 wwCTTTTCwh file2 2 10 792 wwAAATTAtw file2 3 12 1005 syCACTGCAmyc file2 4 13 849 ccAGGCTGGGCtc file2 5 11 1120 mkCCTCCCrms file2 6 10 6 CGCGCGCGCG file2 7 12 1277 dtATTTTTAdww file2 8 11 893 yyCTGCCTCmg file2 9 11 789 cyCTGTCTCwa file2 10 12 733 ccyCCACCTCss file2 11 12 730 wsaCTCTGTCtc ... 7 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_m1 | dyads_m4 | dyads_m1 | dyads_m4 | 0.843 | 0.843 | 9.410 | 0.827 | 0.933 | 2.2697 | 0.93734 | 17 | 17 | 17 | 17 | 1.0000 | 1.0000 | 1.0000 | D | 0 | ccGCCCCCCAGCCCCss | cyGCCCCCCCRCCCCsv | 3 | 1 | 3 | 1 | 1 | 3 | 1 | 1.8571 | 1 |
| dyads_m2 | oligos_7nt_mkv5_m1 | dyads_m2 | oligos_7nt_mkv5_m1 | 0.850 | 0.600 | 10.415 | 0.563 | 0.916 | 2.0065 | 0.91653 | 17 | 12 | 12 | 17 | 0.7059 | 0.7059 | 1.0000 | D | 1 | .wTATTTTTATTT.... | dtATTTTTAdww | 2 | 3 | 1 | 3 | 2 | 2 | 3 | 2.2857 | 2 |
| oligos_7nt_mkv5_m3 | oligos_7nt_mkv5_m5 | oligos_7nt_mkv5_m3 | oligos_7nt_mkv5_m5 | 0.872 | 0.560 | 7.480 | 0.521 | 0.930 | 1.2621 | 0.91174 | 11 | 12 | 9 | 14 | 0.6429 | 0.8182 | 0.7500 | D | -3 | cyCTGTCTC.. | ...CTCTGTCtc | 1 | 4 | 6 | 5 | 3 | 1 | 2 | 3.1429 | 3 |
| oligos_7nt_mkv5_m2 | oligos_7nt_mkv5_m3 | oligos_7nt_mkv5_m2 | oligos_7nt_mkv5_m3 | 0.767 | 0.767 | 8.477 | 0.785 | 0.894 | 2.3376 | 0.90172 | 11 | 11 | 11 | 11 | 1.0000 | 1.0000 | 1.0000 | D | 0 | yyCTGCCTCmg | cyCTGTCTCwa | 5 | 2 | 4 | 2 | 5 | 4 | 4 | 3.7143 | 4 |
| dyads_m4 | oligos_7nt_mkv5_m4 | dyads_m4 | oligos_7nt_mkv5_m4 | 0.758 | 0.535 | 7.780 | 0.542 | 0.892 | 2.5999 | 0.90499 | 17 | 12 | 12 | 17 | 0.7059 | 0.7059 | 1.0000 | D | 5 | .....CCCCCRCCCCsv | ccyCCACCTCss | 6 | 5 | 5 | 4 | 4 | 5 | 5 | 4.8571 | 5 |
| dyads_m3 | oligos_7nt_mkv5_m2 | dyads_m3 | oligos_7nt_mkv5_m2 | 0.771 | 0.404 | 9.694 | 0.376 | 0.870 | 2.8522 | 0.89144 | 21 | 11 | 11 | 21 | 0.5238 | 0.5238 | 1.0000 | D | 3 | ...CyCwGCCTyCC....... | yyCTGCCTCmg | 4 | 6 | 2 | 6 | 6 | 6 | 6 | 5.1429 | 6 |
Host name biow Job started 2014-10-08.084403 Job done 2014-10-08.084406 Seconds 1.21 user 1.21 system 0.07 cuser 2.15 ; csystem 0.36