compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5.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/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_vs_db_jaspar_core_vertebrates
Program version 1.118
Input files
file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf
file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5.tf
Output files
alignments_1ton $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_vs_db_jaspar_core_vertebrates_alignments_1ton.tab
match_table_txt $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_vs_db_jaspar_core_vertebrates.tab
html_index $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_vs_db_jaspar_core_vertebrates_index.html
alignments_1ton_html $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_vs_db_jaspar_core_vertebrates_alignments_1ton.html
match_table_html $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_vs_db_jaspar_core_vertebrates.html
prefix $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_vs_db_jaspar_core_vertebrates
Matrices
file1 1 matrices $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5.tf
file1 1 17 166 rwATGTTGCAATCATtw
file2 263 matrices $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_m5 |
MA0102.3 |
positions_8nt_m5 |
CEBPA |
0.798 |
0.516 |
4.406 |
0.116 |
0.891 |
2.4009 |
0.90040 |
17 |
11 |
11 |
17 |
0.6471 |
0.6471 |
1.0000 |
R |
1 |
.wATGTTGCAAT..... |
KRTTRTGCAAT |
2 |
2 |
2 |
2 |
1 |
1 |
1 |
1.5714 |
1 |
positions_8nt_m5 |
MA0466.1 |
positions_8nt_m5 |
CEBPB |
0.814 |
0.526 |
2.312 |
-0.065 |
0.891 |
2.4087 |
0.90023 |
17 |
11 |
11 |
17 |
0.6471 |
0.6471 |
1.0000 |
R |
2 |
..ATGTTGCAATC.... |
RTKRTGCAATM |
1 |
1 |
3 |
3 |
2 |
2 |
2 |
2.0000 |
2 |
positions_8nt_m5 |
MA0102.2 |
positions_8nt_m5 |
CEBPA |
0.761 |
0.403 |
5.949 |
0.375 |
0.861 |
2.4967 |
0.87586 |
17 |
9 |
9 |
17 |
0.5294 |
0.5294 |
1.0000 |
D |
3 |
...TGTTGCAAT..... |
TtkygCAAy |
3 |
3 |
1 |
1 |
3 |
3 |
3 |
2.4286 |
3 |
Host name rsat
Job started 2014-09-03.190116
Job done 2014-09-03.190126
Seconds 4.21
user 4.22
system 0.12
cuser 5.86
; csystem 0.08