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/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2.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/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_vs_db_regulonDB
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_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 |
|---|
| oligos_6nt_mkv2_shift6 (oligos_6nt_mkv2) |
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; oligos_6nt_mkv2; m=0 (reference); ncol1=11; shift=6; ncol=17; ------taGATCAATrw
; Alignment reference
a 0 0 0 0 0 0 1 2 0 5 0 0 5 5 0 3 2
c 0 0 0 0 0 0 1 1 0 0 0 5 0 0 0 0 0
g 0 0 0 0 0 0 1 1 5 0 0 0 0 0 0 2 1
t 0 0 0 0 0 0 2 1 0 0 5 0 0 0 5 0 2
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| ECK120011229_rc_shift0 (FNR_rc) |
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0.863 |
0.406 |
6.281 |
0.405 |
0.889 |
1.568 |
0.902 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; oligos_6nt_mkv2 versus ECK120011229_rc (FNR_rc); m=1/1; ncol2=14; w=8; offset=-6; strand=R; shift=0; score= 1; TTGATrtwrAtCAa---
; cor=0.863; Ncor=0.406; logoDP=6.281; NIcor=0.405; NsEucl=0.889; SSD=1.568; 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 2 2 6 79 6 29 12 29 35 57 14 2 64 48 0 0 0
c 0 0 5 0 11 11 11 16 3 13 8 58 6 10 0 0 0
g 8 1 72 0 0 23 12 10 28 3 14 10 8 8 0 0 0
t 73 80 0 4 66 20 48 28 17 10 47 13 5 17 0 0 0
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