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/dyads_m5/peak-motifs_dyads_m5.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/footprintDB/footprintDB.motif.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_motifs/dyads_m5/peak-motifs_dyads_m5_vs_db_footprintDB
One-to-n matrix alignment; reference matrix: dyads_m5_shift0 ; 3 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_m5_shift0 (dyads_m5) |
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; dyads_m5; m=0 (reference); ncol1=12; shift=0; ncol=12; rkrCGCTGGAwr
; Alignment reference
a 18 10 25 4 0 1 1 0 0 49 18 13
c 10 10 9 43 1 49 0 0 0 0 7 12
g 14 18 14 3 46 1 0 51 51 1 12 18
t 9 13 3 1 4 0 50 0 0 1 14 8
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2742_PF0055.1_JASPAR_CORE_2009__shift6 (2742_PF0055.1_JASPAR_CORE_2009_) |
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0.840 |
0.420 |
7.225 |
0.398 |
0.864 |
1.331 |
0.889 |
1 |
2 |
1 |
1 |
1 |
1 |
1 |
1.143 |
1 |
; dyads_m5 versus 2742_PF0055.1_JASPAR_CORE_2009_; m=1/2; ncol2=6; w=6; offset=6; strand=D; shift=6; score= 1.1429; ------TGGAAA
; cor=0.840; Ncor=0.420; logoDP=7.225; NIcor=0.398; NsEucl=0.864; SSD=1.331; NSW=0.889; rcor=1; rNcor=2; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.143; match_rank=1
a 0 0 0 0 0 0 0 0 0 6612 6612 6612
c 0 0 0 0 0 0 0 0 0 0 0 0
g 0 0 0 0 0 0 0 6612 6612 0 0 0
t 0 0 0 0 0 0 6612 0 0 0 0 0
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2533_MA0267.1_JASPAR_CORE_2009__rc_shift3 (2533_MA0267.1_JASPAR_CORE_2009__rc) |
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0.777 |
0.453 |
3.736 |
0.146 |
0.862 |
1.876 |
0.866 |
2 |
1 |
2 |
2 |
2 |
2 |
2 |
1.857 |
2 |
; dyads_m5 versus 2533_MA0267.1_JASPAR_CORE_2009__rc; m=2/2; ncol2=7; w=7; offset=3; strand=R; shift=3; score= 1.8571; ---tGCTGGk--
; cor=0.777; Ncor=0.453; logoDP=3.736; NIcor=0.146; NsEucl=0.862; SSD=1.876; NSW=0.866; rcor=2; rNcor=1; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=1.857; match_rank=2
a 0 0 0 14 0 0 0 0 1 5 0 0
c 0 0 0 17 0 100 0 0 6 21 0 0
g 0 0 0 20 100 0 10 100 92 28 0 0
t 0 0 0 49 0 0 90 0 1 45 0 0
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