Available secondary structure formats
The trRosettaRNA server now supports using a secondary structure (SS) as input. Available formats for the input SS are: Note: both two formats do not support high-order base-multiplets. If you need to process data with base-multiplets, please use our standalone package. This package supports a more flexible TXT format for the 2D base-pairing matrix (see an example file).Dot-bracket notation format
The dot-bracket notation, as an most commonly used format, denotes base pairs by matching pairs of parenthesis() and unpaired nucleotides by dots ..
For enhanced flexibility, the trRosettaRNA server accepts extended secondary structure notation. In addition to standard dot-bracket (), it supports other paired bracket types ([], {}, <>) and letter pairs (e.g., Aa, Bb) to denote base pairs.
Furthermore, unpaired nucleotides can be represented by various symbols, including ., ,, _, :, and -.
See an example:
(((((.((.(((.....(((((.....)))))....))).).).)))))
CT(Connectivity Table) format
A CT (Connectivity Table) file contains secondary structure information for a sequence. These files are saved with a CT extension. When submitting a CT file into trRosettaRNA server, the following format must be followed.Start of first line: number of bases in the sequence
End of first line: title of the structure
Each of the following lines provides information about a given base in the sequence. Each base has its own line, with these elements in order:
1. Base number: index
n2. Base (
A, C, G, T, U, N)3. Index
n-14. Index
n+15. Number of the base to which
n is paired. No pairing is indicated by 0.6. Natural numbering (just repeat
n here for convenience).See an example:
71 example
1 A 0 2 0 1
2 C 1 3 70 2
3 C 2 4 69 3
4 C 3 5 68 4
5 G 4 6 0 5
6 C 5 7 0 6
7 A 6 8 0 7
8 A 7 9 64 8
9 G 8 10 63 9
10 G 9 11 61 10
11 C 10 12 60 11
12 C 11 13 59 12
13 G 12 14 27 13
14 A 13 15 0 14
15 C 14 16 25 15
16 G 15 17 24 16
17 G 16 18 23 17
18 C 17 19 22 18
19 A 18 20 0 19
20 A 19 21 0 20
21 A 20 22 0 21
22 G 21 23 18 22
23 C 22 24 17 23
24 C 23 25 16 24
25 G 24 26 15 25
26 C 25 27 0 26
27 C 26 28 13 27
28 G 27 29 44 28
29 C 28 30 43 29
30 U 29 31 42 30
31 G 30 32 41 31
32 G 31 33 40 32
33 U 32 34 0 33
34 G 33 35 0 34
35 C 34 36 0 35
36 A 35 37 0 36
37 A 36 38 0 37
38 G 37 39 0 38
39 U 38 40 0 39
40 C 39 41 32 40
41 C 40 42 31 41
42 A 41 43 30 42
43 G 42 44 29 43
44 C 43 45 28 44
45 C 44 46 58 45
46 A 45 47 57 46
47 C 46 48 56 47
48 G 47 49 55 48
49 C 48 50 54 49
50 U 49 51 0 50
51 U 50 52 0 51
52 C 51 53 0 52
53 G 52 54 0 53
54 G 53 55 49 54
55 C 54 56 48 55
56 G 55 57 47 56
57 U 56 58 46 57
58 G 57 59 45 58
59 G 58 60 12 59
60 G 59 61 11 60
61 C 60 62 10 61
62 G 61 63 0 62
63 C 62 64 9 63
64 U 63 65 8 64
65 C 64 66 0 65
66 A 65 67 0 66
67 U 66 68 0 67
68 G 67 69 4 68
69 G 68 70 3 69
70 G 69 71 2 70
71 U 70 0 0 71
Need more help?
If you have more questions or comments about the server, please email yangjy
sdu.edu.cn.