RNA Data Analysis and Research

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Here we provide instructions to run RADAR in a Windows XP system. Our intent is to show the user how to run RADAR without worrying about setting paths, etc.

First, left click on the Start menu item on the left corner of your screen, then click on Run on the pop-up menu, and then type in cmd so that you are in the DOS environment. Suppose you are now in the directory C:\Documents and Settings\johnsmith (assuming your user name is johnsmith). Use the cd command to change to the C directory as follows:
C:\Documents and Settings\johnsmith>cd ..
C:\Documents and Settings>cd ..
C:\>
Then use the mkdir command to create a new directory, called RADAR, under the C directory as follows:
C:\>mkdir RADAR
Enter the RADAR directory by typing the cd command as follows:
C:\>cd RADAR
Now you are in the RADAR directory.

Download the RADAR.jar file into your RADAR directory. Notice that when this file is saved in your RADAR directory, it is called RADAR.zip. Use the move command to change the file name to RADAR.jar as follows:
C:\RADAR>move RADAR.zip RADAR.jar
Some browsers allow you to save the file with the name RADAR.jar, for which case skip executing the above renaming command.
Also, in Windows, copy all files including sample input and output files into the RADAR directory. If you use the dir command, e.g.
C:\RADAR>dir
you will see all the files and directories in your RADAR directory.

If you do not have Java installed and configured in your computer, go to the Java download webpage (http://java.sun.com/javase/downloads/index.jsp) where you see Java Runtime Environment (JRE) 6 Update 10 download (this is the current version). Click on it and you will be led to a webpage in which you are asked to select a platform. Select Windows. Then you will be led to a new webpage where you see different files. Download Windows Online Installation and save it in your RADAR directory. Then, left (double) click and Run the download file to install Java. Since JRE is now installed, you can run the RADAR.jar program in your RADAR directory by following steps and examples given below.

Following are instructions to execute the RADAR.jar program:  

You can find the general syntax of the command by typing  

java –jar RADAR.jar

The general syntax is as follows:

Usage:

        java –jar RADAR.jar [options]

General options:

-p [ pmatch | imatch | mmatch]

   choose a program from:

        pmatch:        pair-wise comparison & database search;

        imatch:        iterative database search;

        mmatch:        multiple RNA structure alignment with an option for finding common structure;

-d <database>          secondary structure database.

-g <penalty>           gap penalty (default -6). 

-o <output>            file to receive output, default to 'result.txt'.

Options for 'pmatch', 'imatch':

-n <topN>              ouput top 'topN' hits.

-q <query>             query secondary structure.

Options for 'pmatch' :

-s <score_matrix>      file containing position independent score matrices;

                       default is 'scoreMat.structure'.

-G <alignment type>

        T:             global alignment

        F:             local alignment

                       default: F

-m <query type>

query type:

        0:             real structure without IUB code

        1:             pattern structure containing IUB code

                       default: 0

Options for 'imatch':

-R <repeat>            number of iterations (default: 5)

Examples:

• java -jar RADAR.jar  -p pmatch -d test.structDB -q query.struct
  will use the secondary structure in query.struct to search against the structure database test.structDB using the local alignment function. The output is in the default file result.txt, which can be seen here.
• java -jar RADAR.jar -p pmatch -d test.structDB -q query.struct -G T
  will use the secondary structure in query.struct to search against the structure database test.structDB using the global alignment function. The output is in the default file result.txt, which can be seen here.
• java -jar RADAR.jar -p pmatch -d test.structDB -q motif.ire1 -m 1
  will use the pattern structure in motif.ire1 to search against the structure database test.structDB and store the result in the default file result.txt, which can be seen here.
• java -jar RADAR.jar -p mmatch -d test.structDB
  will construct multiple structure alignment for the structures in test.structDB. The output is stored in the default file result.txt, which can be seen here.
• java -jar RADAR.jar -p imatch -d test.structDB -q query.struct -R 2
  will perform an iterative database search with two iterations.