; compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2009_10.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/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_vs_db_jaspar_core_vertebrates ; Program version 1.115 ; Input files ; file2 /home/rsat/rsa-tools/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2009_10.tf ; file1 /home/rsat/rsa-tools/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3.tf ; Output files ; alignments_1ton /home/rsat/rsa-tools/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_vs_db_jaspar_core_vertebrates_alignments_1ton.tab ; match_table_txt /home/rsat/rsa-tools/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_vs_db_jaspar_core_vertebrates.tab ; html_index /home/rsat/rsa-tools/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_vs_db_jaspar_core_vertebrates_index.html ; alignments_1ton_html /home/rsat/rsa-tools/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_vs_db_jaspar_core_vertebrates_alignments_1ton.html ; output_prefix /home/rsat/rsa-tools/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_vs_db_jaspar_core_vertebrates ; match_table_html /home/rsat/rsa-tools/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_vs_db_jaspar_core_vertebrates.html ; Matrices ; file1 1 matrices /home/rsat/rsa-tools/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3.tf ; file2 130 matrices /home/rsat/rsa-tools/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2009_10.tf ; Threshold values ; Parameter Lower Upper ; w 5 none ; offset_rank none 1 ; wr 0.3 none ; cor 0.75 none ; Ncor 0.4 none ; ncor 0.4 none ; 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_m3 MA0137.2 positions_7nt_m3 STAT1 0.975 0.914 8.663 0.878 0.990 0.3072 0.97387 16 15 15 16 0.9375 0.9375 1.0000 R 0 srTTTCYwGGAArts. GRYTTCYDGGAARTG 1 1 2 1 1 1 1 1.1429 1 positions_7nt_m3 MA0144.1 positions_7nt_m3 Stat3 0.963 0.602 9.169 0.595 0.980 0.3905 0.95581 16 10 10 16 0.6250 0.6250 1.0000 D 3 ...TTCYwGGAAr... TTCCaGGAAr 2 2 1 2 2 2 2 1.8571 2 positions_7nt_m3 MA0156.1 positions_7nt_m3 FEV 0.925 0.462 6.770 0.460 0.960 0.6460 0.92896 16 8 8 16 0.5000 0.5000 1.0000 D 6 ......YwGGAArt.. CAGGAArT 3 5 4 4 3 3 3 3.5714 3 positions_7nt_m3 MA0062.2 positions_7nt_m3 GABPA 0.822 0.483 7.163 0.488 0.919 1.6209 0.90997 16 11 10 17 0.5882 0.6250 0.9091 D 6 ......YwGGAArtsr CCGGAAGygv. 5 3 3 3 5 5 5 4.1429 4 positions_7nt_m3 MA0136.1 positions_7nt_m3 ELF5 0.834 0.469 0.177 -0.102 0.938 1.1110 0.91718 16 9 9 16 0.5625 0.5625 1.0000 R 6 ......YwGGAArts. MMGGAWRTW 4 4 5 5 4 4 4 4.2857 5 ; Host name rsat ; Job started 2013-01-11.111058 ; Job done 2013-01-11.111100 ; Seconds 1.53 ; user 1.53 ; system 0.03 ; cuser 1.11 ; csystem 0.05