STRMS

ReadMe file

STRMS Package

1. jgraph.jar, jgrapht-0.5.2.jar - packages needed for drawing the trees created during the alignment stage.
2. prs directory  - examples of configuration files of the program.
3. src - the source code of the package.
4. additional files needed for running - like callMfold.

Preparation and Compilation

Most  of the stages of STRMS can run on Linux or Windows operating systems. The only stage that can run only on Linux - is the stage of folding the target database.

Download and install  Mfold

Requirements

The program is written in Java. For using this program, you need to have JVM installed on the computer.

During the folding stage, temporary files are created by mfold (which are then deleted by a script).  Thus, please make sure that you have enough  memory for placing those files. It is recommended that you will have approximately 10.0 free MB when running the application.

 

How to Run the Program

• Open a Unix shell, and go to the directory that holds the program (e.g. ~/rna/bin/).
• Prepare configuration file for the program (see details in ...).
• From this directory, run the program, with the configuration file as an argument, using the following command:
  > java -Xmx600m -cp .:../jgraph.jar:../jgrapht-0.5.2.jar rna.Main load configfile.pr
   

Program Options and Configuration File

Options

Some results from the article

Results