One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/REGULONDB/regulonDB_2014-04-11.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/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_db_regulonDB
One-to-n matrix alignment; reference matrix: dyads_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 |
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| dyads_m2_shift0 (dyads_m2) |
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; dyads_m2; m=0 (reference); ncol1=20; shift=0; ncol=20; wwwTTGAystagATCAAtww
; Alignment reference
a 12 8 11 1 0 3 27 0 6 6 15 5 26 2 0 28 26 4 11 9
c 4 5 4 0 1 0 0 12 9 4 3 5 1 0 26 0 2 0 2 1
g 3 3 4 1 0 25 0 3 7 3 5 14 1 0 0 0 0 5 0 5
t 9 12 9 26 27 0 1 13 6 15 5 4 0 26 2 0 0 19 15 13
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| ECK120011229_rc_shift3 (FNR_rc) |
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0.915 |
0.641 |
6.428 |
0.637 |
0.948 |
1.060 |
0.962 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; dyads_m2 versus ECK120011229_rc (FNR_rc); m=1/1; ncol2=14; w=14; offset=3; strand=R; shift=3; score= 1; ---TTGATrtwrAtCAa---
; cor=0.915; Ncor=0.641; logoDP=6.428; NIcor=0.637; NsEucl=0.948; SSD=1.060; NSW=0.962; 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 2 2 6 79 6 29 12 29 35 57 14 2 64 48 0 0 0
c 0 0 0 0 0 5 0 11 11 11 16 3 13 8 58 6 10 0 0 0
g 0 0 0 8 1 72 0 0 23 12 10 28 3 14 10 8 8 0 0 0
t 0 0 0 73 80 0 4 66 20 48 28 17 10 47 13 5 17 0 0 0
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