The current
available version is GNU/Linux version.
unzip the file:
gunzip Rnall.tar.Z
tar -xvf Rnall.tar
Running
command:
./Rnall -i filename -o outputfilename
-g/-m [-f] [-t] [-c] [-w 30] [-e -5] [-s 10] [-l 3] [-u 3] [-h -11.7]
-i input file. the input file should
be in the Fasta format
-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
>sequence name: StrNo: start_site
stop_site energy
Structure
Terminator
prediction
>sequence name: StrNo: start_site
stop_site energy T-weight
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 [initially 0]
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 [initially 0]
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
--------------------------------------------
==============================================================================