Install
gunzip Rnall.tar.Z
tar -xvf Rnall.tar
Commands
Running command:
-o output file for predicted RNA local secondary structure
-g for scanning a single genome in the Fasta format
-m for multiple sequences in the Fasta format
-f with non-overlapping structure prediction
-w sliding window size (default 30)
-e energy threshold in the unit of Kcal/mol (default = -5)
-s symmetric mapping score threshold (default = 10)
-l initial hairpin loop size (default = 3)
-u T weight calculation (default = 3)
-h hybridization energy calculation (default = -11.7)
-t terminator prediction
-c output ct file for the predicted structure
Example1:
test.fasta
command: ./Rnall -i filename -o outputfilename -f -w 20 -e -5
output: test.out
Example2:
NC_000908.fasta
command: ./Rnall -i filename -o outputfilename -g -f -w 20 -e -5
output: mg.out
Example 3 (terminator prediction)
terminator129.fasta
command: ./Rnall -i filename -o outputfilename -m -f -t -c -w 30 -e -7.8 -u 3 -h -11.7
output: terminator129.out
Output:
General prediction
Structure
Terminator prediction
hybridization_energy seq=upstream15nt/5stem loop 3stem /3downstream15nt
Structure
Example of an output
General:
StrNo:3 start=4174 stop=4190 dG=-5.6
--------------------------------------------17 dG = -5.6[initially0] Mon Sep 20 13:57:35 2004
1 U 0 2 17 1
2 A 1 3 16 2
3 G 2 4 15 3
4 U 3 5 14 4
5 G 4 6 13 5
6 C 5 7 12 6
7 U 6 8 0 7
8 G 7 9 0 8
9 G 8 10 0 9
10 U 9 11 0 10
11 G 10 12 0 11
12 G 11 13 6 12
13 C 12 14 5 13
14 A 13 15 4 14
15 C 14 16 3 15
16 U 15 17 2 16
17 G 16 18 1 17
--------------------------------------------Terminator:
>ECORELB :StrNo:1 start=26 stop=39 dG=-8.7 Twt=5.77734 hbG=-4.313 seq=GCACCCG%CACUUAA/CCCGC UUCG GCGGG/UUUUUGUU#UUUAUUU
--------------------------------------------14 dG = -8.7[initially0]Mon Sep 20 13:48:02 2004
1 C 0 2 14 1
2 C 1 3 13 2
3 C 2 4 12 3
4 G 3 5 11 4
5 C 4 6 10 5
6 U 5 7 0 6
7 U 6 8 0 7
8 C 7 9 0 8
9 G 8 10 0 9
10 G 9 11 5 10
11 C 10 12 4 11
12 G 11 13 3 12
13 G 12 14 2 13
14 G 13 15 1 14
--------------------------------------------