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BestPal-H |
Calculates best palindrome for given RNA sequence with restrictions.
In this version two types of restriction can be specified:
1) minimal helix length allowed
2) maximal secondary structure length allowed
Method description:
Dynamic programming method without "brahching" of structures with filters using specified restrictions.
Program is provided with viewer.
Output example:
Search for most stable hairpin (imperfect helices included)
FoldRNA Vienna format:
Length: 754 Energy: -7.8 3% in Helices
10 20 30 40 50 60
UGCGGCGGAGACCGUGGUUUAGUGGGCCAAGGGUUCUACGAGUCGGAACACGUGUUAUCU
..((((...((((.((((((...))))))..))))......))))...............
70 80 90 100 110 120
CUUGCGAAGAGUUUAAGGGUCCUGAGGGUGCGGAGUUGUGUUAUCAACCGAACACAGAAG
............................................................
130 140 150 160 170 180
AAUCCCAAAUGAUGAAGCUGAGUCUCAUCAAAGUCGUUAAUGGCUGUCGUCUAGGAAAAA
............................................................
190 200 210 220 230 240
UACAAAACCUGGGCAAAGCAGGGGACUGCACGGUGGACAUUCCGGGCUGUCUUCUCUACA
............................................................
250 260 270 280 290 300
CCAGGACUGGCUCUGCCCCACACCUGACACAUCAGACGCUGCGUAACAUCCACGGGGUCC
............................................................
310 320 330 340 350 360
CAGGCAUAGCCCAGCUCACACUCUCAUCCCUAGCAGAACAUCAUGAAGUCUUGGCAGAAU
............................................................
370 380 390 400 410 420
AUAAGAAAGGAGUUGGAAGCUUUAUAGGCAUGCCGGAAUCACUCUUCUAUUGUUCCCUGC
............................................................
430 440 450 460 470 480
ACGAUCCAGUCACCCCCGGCCCAGCUGGUUAUGUAACAAGUAAGGUCCUCCAGAAAAGUG
............................................................
490 500 510 520 530 540
UGAUCAUUGGAGUGAUUGAGGGUGGAGAUGUGAUGGAAGAGAGGUUGAGGUCAGCACGAG
............................................................
550 560 570 580 590 600
AGACAGCCAAGCGACCCGUCGGGGGCUUCCUGCUGGACGGCUUUCAAGGGGAUCCAGCAG
............................................................
610 620 630 640 650 660
UCACAGAAACCAGACUGCACUUGCUGUCAUCAGUCACUGCAGAGCUGCCAGAGGACAAAC
............................................................
670 680 690 700 710 720
CAAGGCUCAUCUGCGGUGUCAGCCGGCCAGACGAAGUGCUAGAGUGCAUCGAAAGGGGAG
............................................................
730 740 750 760
UGGACUUGUUUGAGAGUUUUUUCCCAUAUCAAGU
..................................
Length = 754
==== structure 1 ====
Start End Energy
3 45 -7.8
Helices: 3
3 - 6 CGGC
42 - 45 GCUG
10 - 13 GACC
32 - 35 UUGG
15 - 20 UGGUUU
24 - 29 ACCGGG
FoldRNA GCG format:
Length: 754 Energy: -7.8
1 U 0 2 0 1
2 G 1 3 0 2
3 C 2 4 45 3
4 G 3 5 44 4
5 G 4 6 43 5
6 C 5 7 42 6
7 G 6 8 0 7
8 G 7 9 0 8
9 A 8 10 0 9
10 G 9 11 35 10
11 A 10 12 34 11
12 C 11 13 33 12
13 C 12 14 32 13
14 G 13 15 0 14
15 U 14 16 29 15
16 G 15 17 28 16
17 G 16 18 27 17
18 U 17 19 26 18
19 U 18 20 25 19
20 U 19 21 24 20
21 A 20 22 0 21
22 G 21 23 0 22
23 U 22 24 0 23
24 G 23 25 20 24
25 G 24 26 19 25
26 G 25 27 18 26
27 C 26 28 17 27
28 C 27 29 16 28
29 A 28 30 15 29
30 A 29 31 0 30
31 G 30 32 0 31
32 G 31 33 13 32
33 G 32 34 12 33
34 U 33 35 11 34
35 U 34 36 10 35
36 C 35 37 0 36
37 U 36 38 0 37
38 A 37 39 0 38
39 C 38 40 0 39
40 G 39 41 0 40
41 A 40 42 0 41
42 G 41 43 6 42
43 U 42 44 5 43
44 C 43 45 4 44
45 G 44 46 3 45
46 G 45 47 0 46
47 A 46 48 0 47
48 A 47 49 0 48
49 C 48 50 0 49
50 A 49 51 0 50
51 C 50 52 0 51
52 G 51 53 0 52
53 U 52 54 0 53
54 G 53 55 0 54
55 U 54 56 0 55
56 U 55 57 0 56
57 A 56 58 0 57
58 U 57 59 0 58
59 C 58 60 0 59
60 U 59 61 0 60
61 C 60 62 0 61
62 U 61 63 0 62
63 U 62 64 0 63
64 G 63 65 0 64
65 C 64 66 0 65
66 G 65 67 0 66
67 A 66 68 0 67
68 A 67 69 0 68
69 G 68 70 0 69
70 A 69 71 0 70
71 G 70 72 0 71
72 U 71 73 0 72
73 U 72 74 0 73
74 U 73 75 0 74
75 A 74 76 0 75
76 A 75 77 0 76
77 G 76 78 0 77
78 G 77 79 0 78
79 G 78 80 0 79
80 U 79 81 0 80
81 C 80 82 0 81
82 C 81 83 0 82
83 U 82 84 0 83
84 G 83 85 0 84
85 A 84 86 0 85
86 G 85 87 0 86
87 G 86 88 0 87
88 G 87 89 0 88
89 U 88 90 0 89
90 G 89 91 0 90
91 C 90 92 0 91
92 G 91 93 0 92
93 G 92 94 0 93
94 A 93 95 0 94
95 G 94 96 0 95
96 U 95 97 0 96
97 U 96 98 0 97
98 G 97 99 0 98
99 U 98 100 0 99
100 G 99 101 0 100
101 U 100 102 0 101
102 U 101 103 0 102
103 A 102 104 0 103
104 U 103 105 0 104
105 C 104 106 0 105
106 A 105 107 0 106
107 A 106 108 0 107
108 C 107 109 0 108
109 C 108 110 0 109
110 G 109 111 0 110
111 A 110 112 0 111
112 A 111 113 0 112
113 C 112 114 0 113
114 A 113 115 0 114
115 C 114 116 0 115
116 A 115 117 0 116
117 G 116 118 0 117
118 A 117 119 0 118
119 A 118 120 0 119
120 G 119 121 0 120
121 A 120 122 0 121
..........