|
How to run the program:
The execute file "RNArip" is in the directory
"./src". Use command
$>./src/RNArip [-option]
to execute the program. The default input file is "input.in". Two
RNA sequences should be input in this file, and both of them are form
"5'" direction. (press enter between two sequences). The result
can be found in two files, which default is "dot.ps" and
"result.out". "dot.ps" is the image file which shows
the base pairing probability and base pairing frequency by random samples.
The other output, including partition function, base pairing probability
and the top 20 sample structure can be found in "result.out".
Options:
[-h]
Show helps.
[-P]
Base pairing probability will be calculated in the result.
[-noPro]
Base pairing probability will be exclude.
[-S]
The program will sample a random single structure.
[-L Numloops]
The program will sample Numloops random structures, and give the base
pairing frequency in the result.
[-noSample]
Sampling function will be exclude.
[-d]
Show details base pairing probabiity, profiles and probability of hybrid
blocks in the result.
[-t topfrequency]
Set the parameter topfrequency, which is the number of top frequency
structure in the result.
[-f psfile]
Specify the image file. Default is "dot.ps".
[-a]
Show all samples.
[-i inputfile]
Specify the image input. Default is "input.in". Note that two
sequences are both from 5' direction.
[-o outputfile]
Specify the image file. Default is "result.out".
[-r profile]
Specify the postscript file of profile.
The input file is following FASTA format. More examples
can be found in /example.
For example, we can use the command:
./src/RNArip -i ./example/test.in -o ./example/test.out -f
./example/test.ps -r ./example/test2.ps -a -d -L 10000
and the result can be found in test.out, test.ps and test2.ps
Another example is
./src/RNArip -i ./example/sodB.in -o ./example/sodB.out -noPro -noprofile
-a -L 10000
and the result can be found in sodB.out.
|
