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/positions_6nt_m1/peak-motifs_positions_6nt_m1.tf -format2 tf -file2 /home/rsat/rsa-tools/public_html/data/motif_databases/DMMPMM_drosophila/idmmpmm_PCM.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/positions_6nt_m1/peak-motifs_positions_6nt_m1_vs_db_IDMMPMM_drosophila
One-to-n matrix alignment; reference matrix: positions_6nt_m1_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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| positions_6nt_m1_shift0 (positions_6nt_m1) |
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; positions_6nt_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; rrrAAAGGGTTAArd
; Alignment reference
a | 338 299 421 1039 1054 828 0 0 0 3 8 840 779 305 274
c | 216 265 122 1 2 15 1 0 0 0 4 1 89 195 240
g | 316 275 453 11 13 223 1073 1071 1074 27 1 232 103 393 287
t | 204 235 78 23 5 8 0 3 0 1044 1061 1 103 181 273
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| Kr_rc_shift1 (Kr_rc) |
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0.969 |
0.711 |
2.138 |
0.095 |
0.953 |
0.544 |
0.975 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; positions_6nt_m1 versus Kr_rc; m=1/1; ncol2=11; w=11; offset=1; strand=R; shift=1; score= 1; -yrAAaGGGTta---
; cor=0.969; Ncor=0.711; logoDP=2.138; NIcor=0.095; NsEucl=0.953; SSD=0.544; NSW=0.975; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
a | 0 41.2239 122.207 250.55 255.546 173.904 0 41.8348 42.4092 16.3753 47.7674 157.647 0 0 0
c | 0 105.041 41.2178 0 10.3333 45.6551 0 0 8.06 5.93559 17.977 28.7388 0 0 0
g | 0 52.2137 85.1102 28.4501 2.06667 35.0057 266.548 226.987 225.999 30.0548 29.6445 40.4672 0 0 0
t | 0 80.521 30.4651 0 11.0536 24.4353 12.4517 10.1783 2.53167 226.634 183.611 52.1469 0 0 0
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