; 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/dyads_m2/peak-motifs_dyads_m2.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/dyads_m2/peak-motifs_dyads_m2_vs_db_footprintDB ; Program version 1.118 ; Input files ; file2 /vh/rsat/rsat/public_html/data/motif_databases/footprintDB/footprintDB.motif.tf ; file1 /vh/rsat/rsat/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2.tf ; Output files ; alignments_1ton /vh/rsat/rsat/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_db_footprintDB_alignments_1ton.tab ; match_table_txt /vh/rsat/rsat/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_db_footprintDB.tab ; html_index /vh/rsat/rsat/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_db_footprintDB_index.html ; alignments_1ton_html /vh/rsat/rsat/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_db_footprintDB_alignments_1ton.html ; match_table_html /vh/rsat/rsat/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_db_footprintDB.html ; prefix /vh/rsat/rsat/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_db_footprintDB ; Matrices ; file1 1 matrices /vh/rsat/rsat/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2.tf ; file1 1 13 55 mkCCTGGCGATwm ; file2 4196 matrices /vh/rsat/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 dyads_m2 4955_brk_DrosophilaTF_1.1_ dyads_m2 4955_brk_DrosophilaTF_1.1_ 0.835 0.449 7.137 0.470 0.901 1.3893 0.88093 13 7 7 13 0.5385 0.5385 1.0000 D 4 ....TGGCGAT.. TGGCGyY 2 1 1 1 2 2 2 1.5714 1 dyads_m2 2843_PF0156.1_JASPAR_CORE_2009_ dyads_m2 2843_PF0156.1_JASPAR_CORE_2009_ 0.839 0.444 0.356 -0.083 0.923 1.3825 0.90762 13 13 9 17 0.5294 0.6923 0.6923 R -4 mkCCTGGCG.... ....CMCCTGGYG 1 2 3 3 1 1 1 1.7143 2 dyads_m2 2606_MA0368.1_JASPAR_CORE_2009_ dyads_m2 2606_MA0368.1_JASPAR_CORE_2009_ 0.760 0.409 1.735 -0.030 0.853 2.0516 0.85531 13 7 7 13 0.5385 0.5385 1.0000 R 2 ..CCTGGCG.... CTTGGCR 3 3 2 2 3 3 3 2.7143 3 ; Host name biow ; Job started 2014-09-05.203939 ; Job done 2014-09-05.204013 ; Seconds 33.05 ; user 33.05 ; system 0.24 ; cuser 0.64 ; csystem 0.16