compare-matrices -v 1 -file1 DemoCompMat.txt -file2 $RSAT/data/motif_databases/JASPAR/jaspar_core_vertebrates_2009_10.tf -format transfac -lth Ncor2 0.7 -lth w 3 -mode profiles -return matrix_id,cor,Ncor,Ncor1,Ncor2,w,offset,strand -o benchmark_result_slow.tab
Program version 1.117
Input files
file2 $RSAT/data/motif_databases/JASPAR/jaspar_core_vertebrates_2009_10.tf
file1 DemoCompMat.txt
Output files
match_table_txt benchmark_result_slow.tab
html_index benchmark_result_slow_index.html
output_prefix benchmark_result_slow
match_table_html benchmark_result_slow.html
Matrices
file1 6 matrices DemoCompMat.txt
file2 130 matrices $RSAT/data/motif_databases/JASPAR/jaspar_core_vertebrates_2009_10.tf
file1 1 12 392 tgCATrACAAwr
file1 2 12 565 wtATGCAAATgw
file1 3 11 246 wtATGyTAAtk
file1 4 20 233 byCwTTGwyATGCAaATGdr
file1 5 21 56 srTATGyGCATATGCAwATrw
file1 6 11 663 AAAAAAAAAAA
file2 1 9 185 GCCcbrrGs
file2 2 6 20 CACGTG
file2 3 6 24 yGCGTG
file2 4 22 24 hwwrGmACryyvtGTwCchrms
file2 5 11 40 CTAGGTGTGAA
file2 6 20 12 drvkcasygrwGcRkrrCsr
file2 7 14 13 TGAmCTTTGmmCyt
file2 8 12 39 rrrTGCAATmcc
file2 9 8 10 TTTsGCGC
file2 10 11 23 TTAyGTAAyrt
file2 11 11 10 waRTdRWkbyc
file2 12 10 28 varcCGGAAr
file2 13 14 27 aAGAyAAGATAAba
file2 14 14 28 bmaasRTAAACAaw
file2 15 8 20 GTAAACAw
file2 16 8 16 vshvwGTA
file2 17 8 23 wwdayATA
file2 18 5 53 gGATr
file2 19 6 63 wGATwg
file2 20 10 53 ymAATCacwg
file2 21 11 18 tAwTGTTTATw
file2 22 12 47 gwwTRTTTdTTY
file2 23 12 31 ksdTrTTTrTwT
file2 24 12 18 krTTACryAAth
file2 25 14 21 gGTTAATwwTTamc
file2 26 12 54 gCGCAGCTGCKy
file2 27 12 20 rAAAryGAAAsy
file2 28 18 12 sGAAAGyGAAAsyrwwwm
file2 29 10 58 CTATTTwTAG
file2 30 12 16 mrrCArCwGswG
file2 31 6 20 yGGGGA
file2 32 10 16 bkAKGGGkrr
file2 33 10 17 rrmCACGTGr
file2 34 11 21 rAsCACGTGGt
file2 35 16 116 myyrrCCAATsrgmrs
file2 36 10 38 GGGrmTTyCC
file2 37 7 17 wTAAktg
file2 38 20 28 sTrGGTCAcsgTGACCyAcW
file2 39 8 31 wgTCAykb
file2 40 30 21 rAAwawwwkcmmmwacymcmcymmcmcymc
file2 41 14 43 TTyACGCwTsAvTk
file2 42 12 18 hcATCAATCAww
file2 43 10 25 wwcwAGGTCA
file2 44 14 36 wwwAwbTAGGTCAr
file2 45 20 11 MCMCmAMmCAmCMmCmmmsm
file2 46 15 10 RGGTCAwcGrGTTCA
file2 47 5 59 AATTA
file2 48 9 20 ACCGGAAGy
file2 49 9 76 rAACAATrG
file2 50 9 31 yhyATTGTs
file2 51 7 49 wsmGGAA
file2 52 12 46 GCCCWTATAwGG
file2 53 9 28 kwwaACAAw
file2 54 7 23 wAACAAT
file2 55 20 10 bayyTCCCAkmaTkCmwyGm
file2 56 6 34 sATGAC
file2 57 12 12 yRCATTCCwsbg
file2 58 12 44 mgAmCAKMTGkT
file2 59 10 29 srTCTGGmwt
file2 60 7 30 CACGTGr
file2 61 6 17 rCCATc
file2 62 6 40 ywTCCk
file2 63 8 51 grCvGTTG
file2 64 10 17 sGGrmwTTCC
file2 65 6 41 CACCTk
file2 66 11 18 GGGGrwyYCCC
file2 67 20 17 msGRACATGyCCGGGCATGT
file2 68 10 18 gGGraTTTCC
file2 69 15 389 sTATAWAwrssssss
file2 70 10 59 wwmCwTwkvt
file2 71 11 12 RGGGTwwCAGc
file2 72 18 9 rrrAacAtwmyGTyCtrw
file2 73 13 67 rGgbCAAAGkyCa
file2 74 17 25 AAAGGTCAAAGGTCAAc
file2 75 15 33 gsmmCCyWrGGkkkm
file2 76 8 15 GCTGAcks
file2 77 14 16 TGGCAssrwGCCAA
file2 78 9 24 ytrAGTRsm
file2 79 7 20 aTACTTA
file2 80 8 38 TAATTrsy
file2 81 6 16 mTCCAC
file2 82 10 20 bwACGTCCGc
file2 83 6 31 cTAATk
file2 84 7 43 mCAAcms
file2 85 13 20 wAATTAATTAwyy
file2 86 9 44 waywTCCkk
file2 87 19 913 ygrCCAsyAGrkGGCrsyr
file2 88 18 2949 ctgskgsggrswGATAAg
file2 89 12 3656 rgsyCAAGGTCA
file2 90 15 1369 ywTTswyATGCAaAt
file2 91 15 669 cywTTGTyaTgcaaA
file2 92 10 613 TTCCaGGAAr
file2 93 14 4090 CCrGyyyrarCCrG
file2 94 14 481 sssgsCbvGGCCTs
file2 95 10 227 mgCACGTGGc
file2 96 11 897 TGTTTrCwywg
file2 97 18 105 GGAAGGAAGGAAGGAAGG
file2 98 11 993 CCGGAAGygvc
file2 99 11 4000 rsWGATAAgrr
file2 100 10 4349 wGGGyGkGGc
file2 101 21 1606 tTCAGcACCatGGACAGckcC
file2 102 11 2000 ktyTGTGGttw
file2 103 15 2085 cayTTCChrGAAryc
file2 104 10 438 msCACGTGGc
file2 105 12 811 TRTTTACwywgg
file2 106 20 475 vkscmaGGtCAcccTGaCCy
file2 107 15 864 strGGgcArAGGkcA
file2 108 11 20 rTGACwmAGCA
file2 109 6 27 ATyAAA
file2 110 7 26 TTTTCCA
file2 111 12 9 yyAATrwTTAAC
file2 112 10 25 mCyCmaGGGA
file2 113 12 24 TGymwGGGGkcr
file2 114 8 13 CAGGAArT
file2 115 8 13 kGTAAACA
file2 116 8 16 CdbwAATk
file2 117 17 23 rGkTCAysgrsAGKTCA
file2 118 8 14 aAGGTCAc
file2 119 6 6912 yTGGCa
file2 120 11 15 yGCGTGGGcGk
file2 121 14 18 GGGGCCcwmGGGGG
file2 122 7 23 cAAGCTT
file2 123 7 42 AGGAAGT
file2 124 8 11 TGACGYcA
file2 125 7 18 TGAmTCA
file2 126 10 35 CCCCkCCCCC
file2 127 9 18 TtkygCAAy
file2 128 18 357 cwrGGTCAsgkTGmCCys
file2 129 8 104 vbACGTGc
file2 130 6 22 CwTTGT
Threshold values
Parameter Lower Upper
w 3 none
ncor2 0.7 none
Column content
1 id1 Identifier of the first matrix
2 id2 Identifier of the second matrix
3 name1 Name of the first matrix
4 name2 Name of the second matrix
5 cor Pearson coefficient of correlation between frequency matrices
6 Ncor Normalized correlation. Ncor = cor * Wr
7 Ncor1 Normalized correlation. Ncor1 = cor * w / w1
8 Ncor2 Normalized correlation. Ncor2 = cor * w / w2
9 w1 Width of the first matrix
10 w2 Width of the second matrix
11 w Alignment length (number of overlapping columns between matrix 1 and matrix 2, as a function of the offset)
12 W Total alignment length (overlapping + non-overlapping columns). W = w1 + w2 - w
13 Wr Relative alignment length (overlap divided by the total alignemnt length). Wr = w/W
14 wr1 Alignment length relative to the width of the first matrix. wr1 = w/w1
15 wr2 Alignment length relative to the width of the second matrix. wr2 = w/w2
16 strand "strand", i.e. orientation of matrix 2 relative to matrix 1 (D=direct; R=reverse)
17 offset shift of the second matrix relative to the first matrix (negative:left; positive: right)
18 consensus1 IUPAC consensus of matrix 1 (dots represent non-aligned columns)
19 consensus2 IUPAC consensus of matrix 2 (dots represent non-aligned columns)
id1 |
id2 |
name1 |
name2 |
cor |
Ncor |
Ncor1 |
Ncor2 |
w1 |
w2 |
w |
W |
Wr |
wr1 |
wr2 |
strand |
offset |
consensus1 |
consensus2 |
oligos_7nt_mkv5_m1 |
MA0067.1 |
oligos_7nt_mkv5_m1 |
Pax2 |
0.702 |
0.468 |
0.468 |
0.702 |
12 |
8 |
8 |
12 |
0.6667 |
0.6667 |
1.0000 |
R |
1 |
.gCATrACA... |
VMRTGACW |
oligos_7nt_mkv5_m1 |
MA0077.1 |
oligos_7nt_mkv5_m1 |
SOX9 |
0.790 |
0.486 |
0.527 |
0.702 |
12 |
9 |
8 |
13 |
0.6154 |
0.6667 |
0.8889 |
D |
4 |
....TrACAAwr |
rAACAATr. |
oligos_7nt_mkv5_m1 |
MA0078.1 |
oligos_7nt_mkv5_m1 |
Sox17 |
0.914 |
0.457 |
0.533 |
0.711 |
12 |
9 |
7 |
14 |
0.5000 |
0.5833 |
0.7778 |
R |
5 |
.....rACAAwr |
SACAATR.. |
oligos_7nt_mkv5_m1 |
MA0084.1 |
oligos_7nt_mkv5_m1 |
SRY |
0.745 |
0.559 |
0.559 |
0.745 |
12 |
9 |
9 |
12 |
0.7500 |
0.7500 |
1.0000 |
D |
2 |
..CATrACAAw. |
kwwaACAAw |
oligos_7nt_mkv5_m1 |
MA0087.1 |
oligos_7nt_mkv5_m1 |
Sox5 |
0.828 |
0.483 |
0.483 |
0.828 |
12 |
7 |
7 |
12 |
0.5833 |
0.5833 |
1.0000 |
D |
4 |
....TrACAAw. |
wAACAAT |
oligos_7nt_mkv5_m1 |
MA0089.1 |
oligos_7nt_mkv5_m1 |
NFE2L1::MafG |
0.842 |
0.421 |
0.421 |
0.842 |
12 |
6 |
6 |
12 |
0.5000 |
0.5000 |
1.0000 |
D |
2 |
..CATrAC.... |
sATGAC |
oligos_7nt_mkv5_m1 |
MA0142.1 |
oligos_7nt_mkv5_m1 |
Pou5f1 |
0.944 |
0.755 |
0.944 |
0.755 |
12 |
15 |
12 |
15 |
0.8000 |
1.0000 |
0.8000 |
R |
-3 |
tgCATrACAAwr |
...TGCATRWSAAWR |
oligos_7nt_mkv5_m1 |
MA0143.1 |
oligos_7nt_mkv5_m1 |
Sox2 |
0.962 |
0.769 |
0.962 |
0.769 |
12 |
15 |
12 |
15 |
0.8000 |
1.0000 |
0.8000 |
R |
-2 |
tgCATrACAAwr |
..TGCATRACAAWR. |
oligos_7nt_mkv5_m1 |
MA0442.1 |
oligos_7nt_mkv5_m1 |
SOX10 |
0.945 |
0.472 |
0.472 |
0.945 |
12 |
6 |
6 |
12 |
0.5000 |
0.5000 |
1.0000 |
R |
6 |
......ACAAwr |
ACAAWG |
oligos_7nt_mkv5_m2 |
MA0075.1 |
oligos_7nt_mkv5_m2 |
Prrx2 |
0.751 |
0.313 |
0.313 |
0.751 |
12 |
5 |
5 |
12 |
0.4167 |
0.4167 |
1.0000 |
D |
7 |
.......AATgw |
AATTA |
oligos_7nt_mkv5_m2 |
MA0132.1 |
oligos_7nt_mkv5_m2 |
Pdx1 |
0.752 |
0.376 |
0.376 |
0.752 |
12 |
6 |
6 |
12 |
0.5000 |
0.5000 |
1.0000 |
D |
5 |
.....CAAATg. |
cTAATk |
oligos_7nt_mkv5_m3 |
MA0075.1 |
oligos_7nt_mkv5_m3 |
Prrx2 |
0.886 |
0.403 |
0.403 |
0.886 |
11 |
5 |
5 |
11 |
0.4545 |
0.4545 |
1.0000 |
R |
6 |
......TAAtk |
TAATT |
oligos_7nt_mkv5_m3 |
MA0132.1 |
oligos_7nt_mkv5_m3 |
Pdx1 |
0.928 |
0.506 |
0.506 |
0.928 |
11 |
6 |
6 |
11 |
0.5455 |
0.5455 |
1.0000 |
D |
5 |
.....yTAAtk |
cTAATk |
positions_7nt_m1 |
MA0077.1 |
positions_7nt_m1 |
SOX9 |
0.766 |
0.345 |
0.345 |
0.766 |
20 |
9 |
9 |
20 |
0.4500 |
0.4500 |
1.0000 |
R |
1 |
.yCwTTGwyA.......... |
CYATTGTTY |
positions_7nt_m1 |
MA0078.1 |
positions_7nt_m1 |
Sox17 |
0.845 |
0.380 |
0.380 |
0.845 |
20 |
9 |
9 |
20 |
0.4500 |
0.4500 |
1.0000 |
D |
0 |
byCwTTGwy........... |
yhyATTGTs |
positions_7nt_m1 |
MA0087.1 |
positions_7nt_m1 |
Sox5 |
0.807 |
0.282 |
0.282 |
0.807 |
20 |
7 |
7 |
20 |
0.3500 |
0.3500 |
1.0000 |
R |
3 |
...wTTGwyA.......... |
ATTGTTW |
positions_7nt_m1 |
MA0089.1 |
positions_7nt_m1 |
NFE2L1::MafG |
0.736 |
0.221 |
0.221 |
0.736 |
20 |
6 |
6 |
20 |
0.3000 |
0.3000 |
1.0000 |
R |
6 |
......GwyATG........ |
GTCATS |
positions_7nt_m1 |
MA0095.1 |
positions_7nt_m1 |
YY1 |
0.756 |
0.227 |
0.227 |
0.756 |
20 |
6 |
6 |
20 |
0.3000 |
0.3000 |
1.0000 |
R |
14 |
..............aATGdr |
GATGGY |
positions_7nt_m1 |
MA0142.1 |
positions_7nt_m1 |
Pou5f1 |
0.989 |
0.742 |
0.742 |
0.989 |
20 |
15 |
15 |
20 |
0.7500 |
0.7500 |
1.0000 |
D |
2 |
..CwTTGwyATGCAaAT... |
ywTTswyATGCAaAt |
positions_7nt_m1 |
MA0143.1 |
positions_7nt_m1 |
Sox2 |
0.948 |
0.711 |
0.711 |
0.948 |
20 |
15 |
15 |
20 |
0.7500 |
0.7500 |
1.0000 |
D |
1 |
.yCwTTGwyATGCAaA.... |
cywTTGTyaTgcaaA |
positions_7nt_m1 |
MA0442.1 |
positions_7nt_m1 |
SOX10 |
0.947 |
0.284 |
0.284 |
0.947 |
20 |
6 |
6 |
20 |
0.3000 |
0.3000 |
1.0000 |
D |
2 |
..CwTTGw............ |
CwTTGT |
positions_7nt_m2 |
MA0033.1 |
positions_7nt_m2 |
FOXL1 |
0.757 |
0.288 |
0.288 |
0.757 |
21 |
8 |
8 |
21 |
0.3810 |
0.3810 |
1.0000 |
R |
10 |
..........TATGCAwA... |
TATRTHWW |
Host name caminante-6.local
Job started 2013-03-05.165441
Job done 2013-03-05.165444
Seconds 3.41
user 3.41
system 0.02
cuser 0
; csystem 0