; compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2.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/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_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/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2.tf ; Output files ; alignments_1ton /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_vs_db_footprintDB_alignments_1ton.tab ; match_table_txt /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_vs_db_footprintDB.tab ; html_index /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_vs_db_footprintDB_index.html ; alignments_1ton_html /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_vs_db_footprintDB_alignments_1ton.html ; match_table_html /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_vs_db_footprintDB.html ; prefix /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_vs_db_footprintDB ; Matrices ; file1 1 matrices /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2.tf ; file1 1 11 7 TsAGGAGTAhw ; 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 oligos_7nt_mkv2 5131_YufM_DBTBS_1.0_ oligos_7nt_mkv2 5131_YufM_DBTBS_1.0_ 0.786 0.572 7.999 0.589 0.872 2.0454 0.87359 11 8 8 11 0.7273 0.7273 1.0000 D 2 ..AGGAGTAh. ArGrGdws 3 2 2 1 3 6 3 2.8571 1 oligos_7nt_mkv2 5047_ZmHOX2a_1__Athamap_20091028_ oligos_7nt_mkv2 5047_ZmHOX2a_1__Athamap_20091028_ 0.825 0.525 0.129 -0.139 0.901 1.3824 0.88123 11 7 7 11 0.6364 0.6364 1.0000 R 0 TsAGGAG.... TTAGGAY 1 4 7 6 1 1 1 3.0000 2 oligos_7nt_mkv2 2780_PF0093.1_JASPAR_CORE_2009_ oligos_7nt_mkv2 2780_PF0093.1_JASPAR_CORE_2009_ 0.778 0.424 9.609 0.424 0.833 2.0000 0.83333 11 6 6 11 0.5455 0.5455 1.0000 D 3 ...GGAGTA.. GGATTA 4 5 1 3 5 2 5 3.5714 3 oligos_7nt_mkv2 3095_NarP_RegulonDB_7.5_ oligos_7nt_mkv2 3095_NarP_RegulonDB_7.5_ 0.789 0.574 0.939 -0.161 0.872 2.0441 0.87363 11 8 8 11 0.7273 0.7273 1.0000 R 2 ..AGGAGTAh. AGRRGTAK 2 1 6 7 2 5 2 3.5714 4 oligos_7nt_mkv2 3094_NarL_RegulonDB_7.5_ oligos_7nt_mkv2 3094_NarL_RegulonDB_7.5_ 0.764 0.555 4.299 0.537 0.857 2.2886 0.86628 11 8 8 11 0.7273 0.7273 1.0000 D 1 .sAGGAGTA.. wakrrkTA 7 3 3 2 4 7 4 4.2857 5 oligos_7nt_mkv2 1771_MA0212.1_JASPAR_CORE_2009_ oligos_7nt_mkv2 1771_MA0212.1_JASPAR_CORE_2009_ 0.767 0.418 1.998 -0.055 0.831 2.0248 0.83230 11 6 6 11 0.5455 0.5455 1.0000 R 3 ...GGAGTA.. GGATTA 5 6 5 5 6 3 6 5.1429 6 oligos_7nt_mkv2 1792_MA0234.1_JASPAR_CORE_2009_ oligos_7nt_mkv2 1792_MA0234.1_JASPAR_CORE_2009_ 0.764 0.417 2.075 -0.055 0.830 2.0388 0.83173 11 6 6 11 0.5455 0.5455 1.0000 R 3 ...GGAGTA.. GGATTA 6 7 4 4 7 4 7 5.5714 7 ; Host name biow ; Job started 2014-09-06.011455 ; Job done 2014-09-06.011526 ; Seconds 29.81 ; user 29.81 ; system 0.27 ; cuser 1.29 ; csystem 0.29