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_m3/peak-motifs_dyads_m3.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_m3/peak-motifs_dyads_m3_vs_db_regulonDB
One-to-n matrix alignment; reference matrix: dyads_m3_shift6 ; 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_m3_shift6 (dyads_m3) |
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; dyads_m3; m=0 (reference); ncol1=11; shift=6; ncol=17; ------ymGATCAAAtw
; Alignment reference
a 0 0 0 0 0 0 2 6 0 11 0 0 11 11 11 2 4
c 0 0 0 0 0 0 3 3 0 0 0 11 0 0 0 2 1
g 0 0 0 0 0 0 2 0 11 0 0 0 0 0 0 0 0
t 0 0 0 0 0 0 4 2 0 0 11 0 0 0 0 7 6
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| ECK120011229_shift0 (FNR) |
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0.863 |
0.406 |
6.313 |
0.409 |
0.903 |
1.216 |
0.924 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; dyads_m3 versus ECK120011229 (FNR); m=1/1; ncol2=14; w=8; offset=-6; strand=D; shift=0; score= 1; tTGaTywayATCAA---
; cor=0.863; Ncor=0.406; logoDP=6.313; NIcor=0.409; NsEucl=0.903; SSD=1.216; NSW=0.924; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
a 17 5 13 47 10 17 28 48 20 66 4 0 80 73 0 0 0
c 8 8 10 14 3 28 10 12 23 0 0 72 1 8 0 0 0
g 10 6 58 8 13 3 16 11 11 11 0 5 0 0 0 0 0
t 48 64 2 14 57 35 29 12 29 6 79 6 2 2 0 0 0
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