One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2.tf -format2 tf -file2 /home/rsat/rsa-tools/public_html/data/motif_databases/JASPAR/jaspar_core_insects_2009_10.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 /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_vs_db_jaspar_core_insects
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_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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| oligos_6nt_mkv4_m2_shift0 (oligos_6nt_mkv4_m2) |
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; oligos_6nt_mkv4_m2; m=0 (reference); ncol1=10; shift=0; ncol=10; acAGATACaw
; Alignment reference
a | 1904 1156 4754 0 4754 0 4754 0 2319 1234
c | 841 1841 0 0 0 0 0 4754 563 1169
g | 931 929 0 4754 0 0 0 0 724 1054
t | 1078 828 0 0 0 4754 0 0 1148 1297
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| MA0246.1_shift2 (so) |
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0.762 |
0.457 |
8.307 |
0.458 |
0.832 |
2.038 |
0.830 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; oligos_6nt_mkv4_m2 versus MA0246.1 (so); m=1/1; ncol2=6; w=6; offset=2; strand=D; shift=2; score= 1; --TGATAC--
; cor=0.762; Ncor=0.457; logoDP=8.307; NIcor=0.458; NsEucl=0.832; SSD=2.038; NSW=0.830; 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 0 27 0 27 0 0 0
c | 0 0 0 0 0 0 0 10 0 0
g | 0 0 1 27 0 1 0 0 0 0
t | 0 0 26 0 0 26 0 3 0 0
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