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_m5/peak-motifs_positions_7nt_m5.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_m5/peak-motifs_positions_7nt_m5_vs_db_footprintDB Program version 1.118 Input files file2 $RSAT/public_html/data/motif_databases/footprintDB/footprintDB.motif.tf 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_m5/peak-motifs_positions_7nt_m5.tf Output files alignments_1ton $RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_vs_db_footprintDB_alignments_1ton.tab match_table_txt $RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_vs_db_footprintDB.tab html_index $RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_vs_db_footprintDB_index.html alignments_1ton_html $RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_vs_db_footprintDB_alignments_1ton.html match_table_html $RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_vs_db_footprintDB.html prefix $RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_vs_db_footprintDB Matrices file1 1 matrices $RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5.tf file1 1 11 6 wkCACTCCAsg file2 4196 matrices $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_m5 | 2858_PF0171.1_JASPAR_CORE_2009_ | positions_7nt_m5 | 2858_PF0171.1_JASPAR_CORE_2009_ | 0.926 | 0.432 | 8.320 | 0.414 | 0.956 | 0.6120 | 0.92098 | 11 | 11 | 7 | 15 | 0.4667 | 0.6364 | 0.6364 | D | 4 | ....CTCCAsg | CTCCAsG.... | 1 | 3 | 2 | 3 | 1 | 2 | 2 | 2.0000 | 1 |
| positions_7nt_m5 | 5958_1a0a_B_3D-footprint_20130124_ | positions_7nt_m5 | 5958_1a0a_B_3D-footprint_20130124_ | 0.924 | 0.420 | 5.834 | 0.422 | 0.961 | 0.3926 | 0.91139 | 11 | 5 | 5 | 11 | 0.4545 | 0.4545 | 1.0000 | D | 6 | ......CCAsg | CCAcg | 2 | 4 | 4 | 2 | 2 | 1 | 1 | 2.2857 | 2 |
| positions_7nt_m5 | 5978_1am9_AB_3D-footprint_20130124_ | positions_7nt_m5 | 5978_1am9_AB_3D-footprint_20130124_ | 0.772 | 0.702 | 12.376 | 0.660 | 0.858 | 2.8403 | 0.88083 | 11 | 10 | 10 | 11 | 0.9091 | 0.9091 | 1.0000 | D | 0 | wkCACTCCAs. | aTCACCCCAC | 6 | 1 | 1 | 1 | 3 | 6 | 6 | 3.4286 | 3 |
| positions_7nt_m5 | 2512_MA0130.1_JASPAR_CORE_2009_ | positions_7nt_m5 | 2512_MA0130.1_JASPAR_CORE_2009_ | 0.800 | 0.437 | 6.779 | 0.396 | 0.875 | 1.4957 | 0.85587 | 11 | 6 | 6 | 11 | 0.5455 | 0.5455 | 1.0000 | D | 4 | ....CTCCAs. | mTCCAC | 5 | 2 | 3 | 4 | 6 | 3 | 5 | 4.0000 | 4 |
| positions_7nt_m5 | 7286_ZAT18_ArabidopsisPBM_20140210_ | positions_7nt_m5 | 7286_ZAT18_ArabidopsisPBM_20140210_ | 0.803 | 0.401 | 3.249 | 0.357 | 0.893 | 1.5048 | 0.87608 | 11 | 10 | 7 | 14 | 0.5000 | 0.6364 | 0.7000 | R | -3 | wkCACTC.... | ...TGCACTH | 4 | 6 | 5 | 5 | 4 | 4 | 3 | 4.4286 | 5 |
| positions_7nt_m5 | 6200_1lo1_A_3D-footprint_20130124_ | positions_7nt_m5 | 6200_1lo1_A_3D-footprint_20130124_ | 0.806 | 0.403 | 1.973 | 0.015 | 0.888 | 1.5614 | 0.87377 | 11 | 10 | 7 | 14 | 0.5000 | 0.6364 | 0.7000 | R | 4 | ....CTCCAsg | CTCNAGG... | 3 | 5 | 6 | 6 | 5 | 5 | 4 | 4.8571 | 6 |
Host name biow Job started 2014-09-05.203449 Job done 2014-09-05.203521 Seconds 29.94 user 29.94 system 0.3 cuser 1.1 ; csystem 0.28