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_8nt_mkv2/peak-motifs_oligos_8nt_mkv2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/REGULONDB/regulonDB_2014-04-11.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/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2_vs_db_regulonDB Program version 1.118 Input files file2 $RSAT/public_html/data/motif_databases/REGULONDB/regulonDB_2014-04-11.tf file1 $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2.tf Output files alignments_1ton $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2_vs_db_regulonDB_alignments_1ton.tab match_table_txt $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2_vs_db_regulonDB.tab html_index $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2_vs_db_regulonDB_index.html alignments_1ton_html $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2_vs_db_regulonDB_alignments_1ton.html match_table_html $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2_vs_db_regulonDB.html prefix $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2_vs_db_regulonDB Matrices file1 1 matrices $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2.tf file1 1 12 3 rwAGAGGGAGws file2 86 matrices $RSAT/public_html/data/motif_databases/REGULONDB/regulonDB_2014-04-11.tf file2 1 13 4 AMkbWWWdmSCAR file2 2 19 11 CTTTCrTTTyvTTTykwTT file2 3 19 15 TRTGkaytwhyykrCTvyk file2 4 15 75 wamawwTwrTTAAma file2 5 18 16 mwkwTTrTsdmwKrthdm file2 6 18 27 hwArTGAATwwThATkCA file2 7 13 7 kywrTGAAACvdk file2 8 12 4 KKWTTrwTGMwT file2 9 17 4 TTCTYCMYdATYKSYkS file2 10 15 4 AmCAATATTGAAArY file2 11 15 57 GTAAArmwrygwaAr ... 76 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 Host name biow Job started 2014-09-06.011352 Job done 2014-09-06.011353 Seconds 1.1 user 1.1 system 0.03 cuser 0 ; csystem 0