One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/10/07/peak-motifs.2014-10-07.150329_2014-10-07.150329_sPZtpE/results/discovered_motifs/dyads_test_vs_ctrl_m3/peak-motifs_dyads_test_vs_ctrl_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/2014/10/07/peak-motifs.2014-10-07.150329_2014-10-07.150329_sPZtpE/results/discovered_motifs/dyads_test_vs_ctrl_m3/peak-motifs_dyads_test_vs_ctrl_m3_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m3_shift0 ; 2 matrices ; sort_field=rank_mean
| Matrix name | Aligned logos | cor |
Ncor |
logoDP |
NIcor |
NsEucl |
SSD |
NSW |
rcor |
rNcor |
rlogoDP |
rNIcor |
rNsEucl |
rSSD |
rNSW |
rank_mean |
match_rank |
Aligned matrices |
|---|
| dyads_test_vs_ctrl_m3_shift0 (dyads_test_vs_ctrl_m3) |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
; dyads_test_vs_ctrl_m3; m=0 (reference); ncol1=15; shift=0; ncol=15; ssGCCbsvsGCCtss
; Alignment reference
a 159 182 24 26 22 9 102 311 14 30 18 36 92 122 179
c 456 389 50 1006 972 486 521 367 395 48 1028 924 202 428 334
g 337 330 1014 67 101 308 384 431 700 1010 56 125 258 392 410
t 166 217 30 19 23 315 111 9 9 30 16 33 566 176 195
|
| MA0003.1_shift2 (TFAP2A) |
 |
0.890 |
0.534 |
4.042 |
0.521 |
0.934 |
0.705 |
0.961 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; dyads_test_vs_ctrl_m3 versus MA0003.1 (TFAP2A); m=1/1; ncol2=9; w=9; offset=2; strand=D; shift=2; score= 1; --GCCcbrrGs----
; cor=0.890; Ncor=0.534; logoDP=4.042; NIcor=0.521; NsEucl=0.934; SSD=0.705; NSW=0.961; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
a 0 0 0 0 0 22 19 55 53 19 9 0 0 0 0
c 0 0 0 185 185 71 57 44 30 16 78 0 0 0 0
g 0 0 185 0 0 46 61 67 91 137 79 0 0 0 0
t 0 0 0 0 0 46 48 19 11 13 19 0 0 0 0
|