BestPal Window help
BestPal_window -
the program for searching best "linear" rna secondary structure for long sequences with a window moving along the sequence.
Method description.
A window with user-defined size moves along the sequence.
For each position of the window the best palindrome is calculated by dynamic programming method without "brahching" of structures.
Only the best variant goes to output file.
BestPal_window parameters:
Window Length - user-defined window size moving along the sequence.
Output example:
Program PestPal (Softberry Inc.) | Version 2.2w
FoldRNA Vienna format:
Length: 590 Energy: -70.1
10 20 30 40 50 60
UAUUAUCGUGUGCAGUUAAAAUUGACUUUUUAAUGCGGCUCCAUUUUUGGGUCGGUGUUU
............................................................
70 80 90 100 110 120
ACUAUUUGAUCAAGGGCUUAAAUAUUUUUGUCUUAAUACGAAAAAACGCACAGAUUUGGU
............................................................
130 140 150 160 170 180
AAAGGCUUAACUUAAAAUUUCAGCGCCCAAUCACCCCCUUCAGAGUUGCCACACGUUGUU
............................................................
190 200 210 220 230 240
ACACUAAGUUAUCGAAACGAACAGCUGAUUUUUGUUUUGUAAUAUUUGAGGUUGGUUUUU
............................................................
250 260 270 280 290 300
GUUGGCUGAAAUAUUAUUACAUUAAAUUAGAUAUGGACCUUUUACUUCAAAGCGUUUGAC
............................................................
310 320 330 340 350 360
AAGUUGAACAUCAAACGGAAAUCUAUUAUAGCCCCAAUUGGCGAGACCAUCAAAUAAUCA
..............................(((....((((.(((((((((......(((
370 380 390 400 410 420
UUGGAAAACAACCUGAGAUGAGUUUUCCAGACAAGGCGGAGCGCAAAAAGUGCUGGAACA
(((.....)))..))))))).)))))))))....))).......................
430 440 450 460 470 480
ACCGGGACGAGUAUUGGAAAUGUCUCGAGGAGCACGCCCCAAAGCACAGUUCUACCAGUG
............................................................
490 500 510 520 530 540
GGGAAAAGGUACCAACCCCCUGCCAGAGUCUUCGCAAAUCAUUUGAGCAAUCCUGCCCUG
............................................................
550 560 570 580 590
GUCAAUGGGUAAAGCACUUCGACCGCAAGCGUACUUAUGACCAGUUUAAG
..................................................
FoldRNA GCG format:
Length: 590 Energy: -70.1
1 U 0 2 0 1
2 A 1 3 0 2
3 U 2 4 0 3
4 U 3 5 0 4
5 A 4 6 0 5
6 U 5 7 0 6
7 C 6 8 0 7
8 G 7 9 0 8
9 U 8 10 0 9
10 G 9 11 0 10
11 U 10 12 0 11
12 G 11 13 0 12
13 C 12 14 0 13
14 A 13 15 0 14
15 G 14 16 0 15
16 U 15 17 0 16
17 U 16 18 0 17
18 A 17 19 0 18
19 A 18 20 0 19
20 A 19 21 0 20
21 A 20 22 0 21
22 U 21 23 0 22
23 U 22 24 0 23
24 G 23 25 0 24
25 A 24 26 0 25
26 C 25 27 0 26
27 U 26 28 0 27
28 U 27 29 0 28
29 U 28 30 0 29
30 U 29 31 0 30
31 U 30 32 0 31
32 A 31 33 0 32
33 A 32 34 0 33
34 U 33 35 0 34
35 G 34 36 0 35
36 C 35 37 0 36
37 G 36 38 0 37
38 G 37 39 0 38
39 C 38 40 0 39
40 U 39 41 0 40
...
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