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comparison test-data/dreme1.txt @ 1:793225b11202 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
author iuc
date Wed, 25 Apr 2018 12:13:08 -0400
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0:a0fa4efeeee3 1:793225b11202
1 # DREME 4.12.0
2 # command: dreme -oc dreme_out -rna -norc -p dreme_test_sites.fa -e 0.05 -mink 3 -maxk 8
3 # positives: 1000 from dreme_test_sites.fa (Thu Apr 19 19:09:45 CEST 2018)
4 # negatives: 1000 from shuffled positives
5 # host: ThinkPad-T450s
6 # when: Thu Apr 19 19:11:17 CEST 2018
7
8 MEME version 4.12.0
9
10 ALPHABET "RNA" RNA-LIKE
11 A "Adenine" CC0000
12 C "Cytosine" 0000CC
13 G "Guanine" FFB300
14 U "Uracil" 008000
15 N "Any base" = ACGU
16 X = ACGU
17 . = ACGU
18 V "Not U" = ACG
19 H "Not G" = ACU
20 D "Not C" = AGU
21 B "Not A" = CGU
22 M "Amino" = AC
23 R "Purine" = AG
24 W "Weak" = AU
25 S "Strong" = CG
26 Y "Pyrimidine" = CU
27 K "Keto" = GU
28 T = U
29 END ALPHABET
30
31 Background letter frequencies (from dataset):
32 A 0.221 C 0.245 G 0.221 U 0.312
33
34
35 MOTIF UUYUCY DREME-1
36
37 # Word Pos Neg P-value E-value
38 # BEST UUYUCY 387 210 2.6e-018 1.2e-013
39 # UUUUCC 147 75 1.8e-007 8.1e-003
40 # UUUUCU 155 94 2.2e-005 1.0e+000
41 # UUCUCU 94 51 1.3e-004 6.1e+000
42 # UUCUCC 75 42 1.1e-003 5.0e+001
43
44 letter-probability matrix: alength= 4 w= 6 nsites= 459 E= 1.2e-013
45 0.000000 0.000000 0.000000 1.000000
46 0.000000 0.000000 0.000000 1.000000
47 0.000000 0.294118 0.000000 0.705882
48 0.000000 0.000000 0.000000 1.000000
49 0.000000 1.000000 0.000000 0.000000
50 0.000000 0.474946 0.000000 0.525054
51
52
53 MOTIF YAGG DREME-2
54
55 # Word Pos Neg P-value E-value
56 # BEST YAGG 600 416 1.1e-016 5.1e-012
57 # CAGG 441 304 1.5e-010 6.6e-006
58 # UAGG 232 165 1.1e-004 4.7e+000
59
60 letter-probability matrix: alength= 4 w= 4 nsites= 793 E= 5.1e-012
61 0.000000 0.692308 0.000000 0.307692
62 1.000000 0.000000 0.000000 0.000000
63 0.000000 0.000000 1.000000 0.000000
64 0.000000 0.000000 1.000000 0.000000
65
66
67 MOTIF GAAGAW DREME-3
68
69 # Word Pos Neg P-value E-value
70 # BEST GAAGAW 81 22 8.2e-010 3.4e-005
71 # GAAGAU 45 7 2.4e-008 9.9e-004
72 # GAAGAA 40 16 7.9e-004 3.3e+001
73
74 letter-probability matrix: alength= 4 w= 6 nsites= 89 E= 3.4e-005
75 0.000000 0.000000 1.000000 0.000000
76 1.000000 0.000000 0.000000 0.000000
77 1.000000 0.000000 0.000000 0.000000
78 0.000000 0.000000 1.000000 0.000000
79 1.000000 0.000000 0.000000 0.000000
80 0.494382 0.000000 0.000000 0.505618
81
82
83 MOTIF SMUGGA DREME-4
84
85 # Word Pos Neg P-value E-value
86 # BEST SMUGGA 110 47 9.1e-008 3.7e-003
87 # GAUGGA 22 6 1.7e-003 7.1e+001
88 # GCUGGA 33 14 3.6e-003 1.5e+002
89 # CCUGGA 32 15 8.6e-003 3.5e+002
90 # CAUGGA 29 13 9.1e-003 3.7e+002
91
92 letter-probability matrix: alength= 4 w= 6 nsites= 119 E= 3.7e-003
93 0.000000 0.529412 0.470588 0.000000
94 0.428571 0.571429 0.000000 0.000000
95 0.000000 0.000000 0.000000 1.000000
96 0.000000 0.000000 1.000000 0.000000
97 0.000000 0.000000 1.000000 0.000000
98 1.000000 0.000000 0.000000 0.000000
99
100
101 # Stopping reason: E-value threshold exceeded
102 # Running time: 13.45 seconds