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_6nt_m3/peak-motifs_positions_6nt_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_6nt_m3/peak-motifs_positions_6nt_m3_vs_db_DMMPMM_drosophila
One-to-n matrix alignment; reference matrix: positions_6nt_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_6nt_m3_shift0 (positions_6nt_m3) |
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; positions_6nt_m3; m=0 (reference); ncol1=10; shift=0; ncol=10; wrCAGGTAra
; Alignment reference
a | 1036 986 0 3557 0 0 0 3557 1228 1214
c | 764 745 3557 0 0 0 0 0 538 770
g | 860 1059 0 0 3557 3557 0 0 1249 762
t | 897 767 0 0 0 0 3557 0 542 811
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| sna_shift0 (sna) |
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0.788 |
0.709 |
6.730 |
0.685 |
0.896 |
1.767 |
0.902 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; positions_6nt_m3 versus sna; m=1/1; ncol2=9; w=9; offset=0; strand=D; shift=0; score= 1; AdCArGTdr-
; cor=0.788; Ncor=0.709; logoDP=6.730; NIcor=0.685; NsEucl=0.896; SSD=1.767; NSW=0.902; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
a | 9 4 0 10 4 0 0 3 3 0
c | 2 0 11 0 0 0 0 0 2 0
g | 0 4 0 1 6 11 2 5 6 0
t | 0 3 0 0 1 0 9 3 0 0
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