One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $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 -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/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_vs_db/peak-motifs_motifs_vs_db_regulonDB.tab
One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift2 ; 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_m2_shift2 (positions_6nt_m2) |
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; positions_6nt_m2; m=0 (reference); ncol1=11; shift=2; ncol=19; --TCCCCTAGCGC------
; Alignment reference
a 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
c 0 0 0 1 1 1 1 0 0 0 1 0 1 0 0 0 0 0 0
g 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0
t 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
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| ECK120026325_shift0 (HipB) |
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0.850 |
0.492 |
11.098 |
0.472 |
0.901 |
2.375 |
0.892 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; positions_6nt_m2 versus ECK120026325 (HipB); m=1/1; ncol2=19; w=11; offset=-2; strand=D; shift=0; score= 1; TATCCbbKWdhGMGGATAA
; cor=0.850; Ncor=0.492; logoDP=11.098; NIcor=0.472; NsEucl=0.901; SSD=2.375; NSW=0.892; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
a 0 4 0 0 0 0 0 0 3 1 2 0 1 0 0 4 0 4 4
c 0 0 0 4 4 2 2 0 0 0 1 0 3 0 0 0 0 0 0
g 0 0 0 0 0 1 1 1 0 2 0 4 0 4 4 0 0 0 0
t 4 0 4 0 0 1 1 3 1 1 1 0 0 0 0 0 4 0 0
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