compare-matrices -v 1 -mode matches -format1 transfac -file1 11/regulon11.rm.fna.peaks-rm/results/discovered_motifs/peaks_motifs_discovered.tf -format2 transfac -file2 $RSAT/_footprintDB/footprintDB.transfac.plants.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 11/regulon11.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB.tab Program version 1.118 Slow mode Input files file2 $RSAT/_footprintDB/footprintDB.transfac.plants.motif.tf file1 11/regulon11.rm.fna.peaks-rm/results/discovered_motifs/peaks_motifs_discovered.tf Output files alignments_1ton 11/regulon11.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB_alignments_1ton.tab match_table_txt 11/regulon11.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB.tab html_index 11/regulon11.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB_index.html alignments_1ton_html 11/regulon11.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB_alignments_1ton.html match_table_html 11/regulon11.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB.html prefix 11/regulon11.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB Matrices file1 4 matrices 11/regulon11.rm.fna.peaks-rm/results/discovered_motifs/peaks_motifs_discovered.tf file1 1 14 23 bwGTTbtwtCAAam file1 2 23 32 hhAAAkwwmwwtwAmwwdAAcvw file1 3 30 21 kkgcArwdwtwTcAaawwarawyTwAaaaw file1 4 28 27 kwwTTswTkhwdmAAmwwaawmwmyrwk file2 1055 matrices $RSAT/_footprintDB/footprintDB.transfac.plants.motif.tf file2 1 16 5 TCATTCCACGTAGATr file2 2 8 5 awmAGTTr file2 3 8 3 rkTAGTTr file2 4 8 5 wamaGTTr file2 5 8 1 GTTAGTTA file2 6 8 2 kwCwGTTr file2 7 8 2 GTTAGTTr file2 8 8 6 wwmaGTTr file2 9 8 2 rsTkGTTr file2 10 8 8 RkTwGKTr file2 11 8 1 TACTGTTG ... 1045 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_test_vs_ctrl_m1 | MYBAS1_M00798_TRANSFAC | dyads_test_vs_ctrl_m1 | MYBAS1_M00798_TRANSFAC | 0.884 | 0.497 | 0.018 | -0.070 | 0.967 | 0.5871 | 0.93980 | 14 | 11 | 9 | 16 | 0.5625 | 0.6429 | 0.8182 | R | -2 | bwGTTbtwt..... | ..CMGTTRBSG | 2 | 1 | 6 | 5 | 1 | 2 | 1 | 2.5714 | 1 |
| dyads_test_vs_ctrl_m1 | MYB2_MYB2_Athamap | dyads_test_vs_ctrl_m1 | MYB2_MYB2_Athamap | 0.899 | 0.419 | 0.285 | -0.026 | 0.962 | 0.5312 | 0.92638 | 14 | 8 | 7 | 15 | 0.4667 | 0.5000 | 0.8750 | R | -1 | bwGTTbt....... | .BVGTTDB | 1 | 5 | 3 | 3 | 3 | 1 | 2 | 2.5714 | 2 |
| dyads_test_vs_ctrl_m2 | PK22848.1_M0587_1.02_CISBP | dyads_test_vs_ctrl_m2 | PK22848.1_M0587_1.02_CISBP | 0.755 | 0.427 | 2.066 | 0.409 | 0.939 | 1.5791 | 0.93165 | 23 | 13 | 13 | 23 | 0.5652 | 0.5652 | 1.0000 | D | 0 | hhAAAkwwmwwtw.......... | mmAAATTTwaawa | 6 | 4 | 1 | 2 | 2 | 6 | 4 | 3.5714 | 3 |
| dyads_test_vs_ctrl_m1 | ZFP5_M0369_1.02_CISBP | dyads_test_vs_ctrl_m1 | ZFP5_M0369_1.02_CISBP | 0.817 | 0.467 | 0.031 | -0.049 | 0.945 | 0.8804 | 0.91707 | 14 | 8 | 8 | 14 | 0.5714 | 0.5714 | 1.0000 | R | 1 | .wGTTbtwt..... | ASWTHVMW | 3 | 3 | 5 | 4 | 4 | 3 | 3 | 3.5714 | 4 |
| dyads_test_vs_ctrl_m1 | ZFP8_M0371_1.02_CISBP | dyads_test_vs_ctrl_m1 | ZFP8_M0371_1.02_CISBP | 0.764 | 0.491 | 1.129 | 0.510 | 0.914 | 1.5562 | 0.90199 | 14 | 9 | 9 | 14 | 0.6429 | 0.6429 | 1.0000 | D | 1 | .wGTTbtwtC.... | wswthvmdy | 5 | 2 | 2 | 1 | 6 | 5 | 6 | 3.8571 | 5 |
| dyads_test_vs_ctrl_m1 | Gam1_MA0034.1_JASPAR | dyads_test_vs_ctrl_m1 | Gam1_MA0034.1_JASPAR | 0.808 | 0.404 | 0.073 | -0.084 | 0.937 | 1.0106 | 0.91115 | 14 | 10 | 8 | 16 | 0.5000 | 0.5714 | 0.8000 | R | -2 | bwGTTbtw...... | ..CGGTTRYC | 4 | 6 | 4 | 6 | 5 | 4 | 5 | 4.8571 | 6 |
Host name baobab.eead.csic.es Job started 2016-06-03.165013 Job done 2016-06-03.165101 Seconds 46.32 user 46.32 system 0.27 cuser 2.01 ; csystem 0.27