; compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.094519_2014-09-03.094519_gM9GBj/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.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/wwwrun/2014/09/03/peak-motifs.2014-09-03.094519_2014-09-03.094519_gM9GBj/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2_vs_db_jaspar_core_vertebrates ; Program version 1.118 ; Input files ; file2 /home/rsat/rsat/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf ; file1 /home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.094519_2014-09-03.094519_gM9GBj/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2.tf ; Output files ; alignments_1ton /home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.094519_2014-09-03.094519_gM9GBj/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2_vs_db_jaspar_core_vertebrates_alignments_1ton.tab ; match_table_txt /home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.094519_2014-09-03.094519_gM9GBj/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2_vs_db_jaspar_core_vertebrates.tab ; html_index /home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.094519_2014-09-03.094519_gM9GBj/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2_vs_db_jaspar_core_vertebrates_index.html ; alignments_1ton_html /home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.094519_2014-09-03.094519_gM9GBj/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2_vs_db_jaspar_core_vertebrates_alignments_1ton.html ; match_table_html /home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.094519_2014-09-03.094519_gM9GBj/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2_vs_db_jaspar_core_vertebrates.html ; prefix /home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.094519_2014-09-03.094519_gM9GBj/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2_vs_db_jaspar_core_vertebrates ; Matrices ; file1 1 matrices /home/rsat/rsat/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.094519_2014-09-03.094519_gM9GBj/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2.tf ; file1 1 14 610 mtGTTGAGCAATmw ; file2 263 matrices /home/rsat/rsat/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf ; file2 1 11 26 wwyTGyGGTww ; file2 2 9 185 GCCcbrrGs ; file2 3 6 20 CACGTG ; file2 4 6 24 yGCGTG ; file2 5 22 24 hwwrGmACryyvtGTwCchrms ; file2 6 11 40 CTAGGTGTGAA ; file2 7 20 12 drvkcasygrwGcRkrrCsr ; file2 8 14 13 TGAmCTTTGmmCyt ; file2 9 12 16 bbkGrTGACGym ; file2 10 12 39 rrrTGCAATmcc ; file2 11 8 10 TTTsGCGC ; ... 253 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_8nt_m2 MA0102.1 positions_8nt_m2 Cebpa 0.825 0.605 6.398 0.593 0.911 1.9561 0.91009 14 12 11 15 0.7333 0.7857 0.9167 D 3 ...TTGAGCAATmw TtkygCAAyvy. 3 3 1 1 1 3 2 2.0000 1 positions_8nt_m2 MA0133.1 positions_8nt_m2 BRCA1 0.857 0.428 0.165 -0.127 0.939 0.8571 0.90648 14 7 7 14 0.5000 0.5000 1.0000 R 0 mtGTTGA....... SKGTTGK 1 5 5 5 2 1 1 2.8571 2 positions_8nt_m2 MA0102.2 positions_8nt_m2 CEBPA 0.835 0.537 6.397 0.520 0.896 1.8794 0.89229 14 9 9 14 0.6429 0.6429 1.0000 D 3 ...TTGAGCAAT.. TtkygCAAy 2 4 2 2 5 2 4 3.0000 3 positions_8nt_m2 MA0102.3 positions_8nt_m2 CEBPA 0.820 0.644 4.290 0.128 0.900 2.2040 0.90457 14 11 11 14 0.7857 0.7857 1.0000 R 1 .tGTTGAGCAAT.. KRTTRTGCAAT 4 1 3 3 3 4 3 3.0000 4 positions_8nt_m2 MA0466.1 positions_8nt_m2 CEBPB 0.802 0.630 2.569 -0.025 0.891 2.4081 0.90025 14 11 11 14 0.7857 0.7857 1.0000 R 2 ..GTTGAGCAATm. RTKRTGCAATM 5 2 4 4 4 5 5 4.1429 5 ; Host name rsat ; Job started 2014-09-03.101551 ; Job done 2014-09-03.101601 ; Seconds 3.88 ; user 3.88 ; system 0.13 ; cuser 5.96 ; csystem 0.13