One-to-n alignments
Command: compare-matrices -v 1 -format transfac -file $RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -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/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab
One-to-n matrix alignment; reference matrix: dyads_m1_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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| dyads_m1_shift0 (dyads_m1) |
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; dyads_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; wyATCGCCAGCGygg
; Alignment reference
a 10 6 28 2 0 1 1 0 32 0 1 2 7 6 5
c 8 12 2 3 29 0 31 34 1 0 32 0 9 8 8
g 5 4 3 5 2 33 1 0 0 33 1 29 2 14 16
t 11 12 1 24 3 0 1 0 1 1 0 3 16 6 5
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| dyads_m2_rc_shift0 (dyads_m2_rc) |
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0.802 |
0.695 |
3.149 |
0.070 |
0.920 |
2.185 |
0.916 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; dyads_m1 versus dyads_m2_rc; m=1/1; ncol2=13; w=13; offset=0; strand=R; shift=0; score= 1; kwATCGCCAGGmk--
; cor=0.802; Ncor=0.695; logoDP=3.149; NIcor=0.070; NsEucl=0.920; SSD=2.185; NSW=0.916; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
a 13 17 50 3 1 3 2 2 47 4 3 21 13 0 0
c 12 10 0 1 52 0 50 52 3 3 7 16 10 0 0
g 15 13 2 1 0 52 0 1 1 45 44 11 15 0 0
t 15 15 3 50 2 0 3 0 4 3 1 7 17 0 0
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