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_m3/peak-motifs_positions_7nt_m3.tf -format2 tf -file2 /home/rsat/rsa-tools/public_html/data/motif_databases/DMMPMM_drosophila/dmmpmm_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_m3/peak-motifs_positions_7nt_m3_vs_db_DMMPMM_drosophila
One-to-n matrix alignment; reference matrix: positions_7nt_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 |
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| positions_7nt_m3_shift0 (positions_7nt_m3) |
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; positions_7nt_m3; m=0 (reference); ncol1=12; shift=0; ncol=13; yckCTCkCKCtc-
; Alignment reference
a | 576 599 23 0 0 0 0 0 0 0 798 520 0
c | 1281 2822 4 5043 0 5043 0 5043 0 5043 816 2766 0
g | 950 581 1788 0 0 0 1653 0 1290 0 972 752 0
t | 2236 1041 3228 0 5043 0 3390 0 3753 0 2457 1005 0
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| Trl_shift0 (Trl) |
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0.821 |
0.757 |
3.792 |
0.727 |
0.924 |
1.679 |
0.930 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; positions_7nt_m3 versus Trl; m=1/1; ncol2=13; w=12; offset=0; strand=D; shift=0; score= 1; TtkykCTCtCtct
; cor=0.821; Ncor=0.757; logoDP=3.792; NIcor=0.727; NsEucl=0.924; SSD=1.679; NSW=0.930; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
a | 10 15 4 0 7 0 4 2 6 13 9 4 18
c | 10 8 19 41 3 72 0 56 12 56 16 47 3
g | 0 13 24 10 27 5 11 8 9 1 6 9 14
t | 57 41 30 26 40 0 62 11 50 7 46 17 42
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