; compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.194903_2014-09-05.194903_oebJl9/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3.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/apache/2014/09/05/peak-motifs.2014-09-05.194903_2014-09-05.194903_oebJl9/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_vs_db_jaspar_core_vertebrates ; Program version 1.118 ; Input files ; file2 /vh/rsat/rsat/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf ; file1 /vh/rsat/rsat/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.194903_2014-09-05.194903_oebJl9/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3.tf ; Output files ; alignments_1ton /vh/rsat/rsat/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.194903_2014-09-05.194903_oebJl9/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_vs_db_jaspar_core_vertebrates_alignments_1ton.tab ; match_table_txt /vh/rsat/rsat/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.194903_2014-09-05.194903_oebJl9/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_vs_db_jaspar_core_vertebrates.tab ; html_index /vh/rsat/rsat/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.194903_2014-09-05.194903_oebJl9/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_vs_db_jaspar_core_vertebrates_index.html ; alignments_1ton_html /vh/rsat/rsat/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.194903_2014-09-05.194903_oebJl9/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_vs_db_jaspar_core_vertebrates_alignments_1ton.html ; match_table_html /vh/rsat/rsat/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.194903_2014-09-05.194903_oebJl9/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_vs_db_jaspar_core_vertebrates.html ; prefix /vh/rsat/rsat/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.194903_2014-09-05.194903_oebJl9/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3_vs_db_jaspar_core_vertebrates ; Matrices ; file1 1 matrices /vh/rsat/rsat/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.194903_2014-09-05.194903_oebJl9/results/discovered_motifs/positions_8nt_m3/peak-motifs_positions_8nt_m3.tf ; file1 1 12 34 dsTGGTAATTcw ; file2 263 matrices /vh/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_m3 MA0075.1 positions_8nt_m3 Prrx2 0.983 0.410 1.577 0.069 0.979 0.2107 0.93509 12 5 5 12 0.4167 0.4167 1.0000 R 5 .....TAATT.. TAATT 1 2 2 2 1 1 1 1.4286 1 positions_8nt_m3 MA0125.1 positions_8nt_m3 Nobox 0.877 0.472 3.962 0.501 0.942 0.8072 0.90924 12 8 7 13 0.5385 0.5833 0.8750 D 5 .....TAATTcw TAATTrs. 2 1 1 1 2 2 2 1.5714 2 ; Host name biow ; Job started 2014-09-05.195202 ; Job done 2014-09-05.195204 ; Seconds 2.15 ; user 2.15 ; system 0.06 ; cuser 0.47 ; csystem 0.08