One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2.tf -format2 tf -file2 /home/rsat/rsa-tools/public_html/data/motif_databases/DMMPMM_drosophila/idmmpmm_PCM.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 /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_vs_db_IDMMPMM_drosophila
One-to-n matrix alignment; reference matrix: positions_7nt_m2_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 |
|---|
| positions_7nt_m2_shift0 (positions_7nt_m2) |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
; positions_7nt_m2; m=0 (reference); ncol1=20; shift=0; ncol=20; wwAATwwwwwwwwTwTwAww
; Alignment reference
a | 1198 1305 2806 3297 188 1654 1534 1888 2133 1805 2054 1138 2494 149 1670 193 1340 2771 1162 1178
c | 661 685 268 118 85 58 57 49 77 64 46 89 59 109 39 140 77 282 659 648
g | 708 645 154 125 98 62 50 47 69 51 73 79 75 114 59 130 74 234 685 665
t | 1192 1124 531 219 3388 1985 2118 1775 1480 1839 1586 2453 1131 3387 1991 3296 2268 472 1253 1268
|
| bab1_rc_shift0 (bab1_rc) |
 |
0.765 |
0.535 |
2.102 |
0.202 |
0.928 |
2.036 |
0.927 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; positions_7nt_m2 versus bab1_rc; m=1/1; ncol2=14; w=14; offset=0; strand=R; shift=0; score= 1; AywATwATAwAtAT------
; cor=0.765; Ncor=0.535; logoDP=2.102; NIcor=0.202; NsEucl=0.928; SSD=2.036; NSW=0.927; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
a | 23.8333 5.95833 15.5833 30.5556 3.66667 17.4167 31.1667 3.66667 25.3611 12.5278 24.1389 7.33333 27.1944 1.22222 0 0 0 0 0 0
c | 3.36111 9.625 0 0 6.72222 0.611111 1.83333 0 0 0.611111 3.36111 6.11111 0.916667 3.05556 0 0 0 0 0 0
g | 0.916667 0.763889 1.22222 1.83333 0 1.83333 0 0.611111 1.22222 0 1.83333 3.66667 3.36111 5.5 0 0 0 0 0 0
t | 4.88889 16.6528 16.1944 0.611111 22.6111 13.1389 0 28.7222 6.41667 19.8611 3.66667 15.8889 1.52778 23.2222 0 0 0 0 0 0
|