RNAView Program

The RNAView program generates 2-dimensional displays of RNA/DNA secondary structures with tertiary interactions. RNAView automatically identifies and classifies the types of base pairs that are formed in nucleic acid structures, fully implementing Leontis and Westhof's ( RNA (2001) 7, 499-512), convention for edge-to-edge hydrogen bonding interactions.

[Yang, H., Jossinet, F., Leontis, N., Chen, L., Westbrook, J., Berman, H.M., Westhof, E. (2003). Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Research 31.13: 3450-3460.]

 Download RNAView

The program has been tested in Linux, UNIX, SUN, and MAC systems

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How to install the program:

The program can be installed in any directory (for example /?/?/?/)

1. Unpack the program package in the directory that you desire (e.g. /?/?/?/ ).
   TYPE
   

     zcat RNAVIEW.tar.gz | tar xvf - 

2. Install the program
   Go to the /?/?/?/RNAVIEW/ directory
   Type
   

     make 

   An executable file rnaview will be placed in the directory /?/?/?/RNAVIEW/bin/
   
   

3. Define the environment variable RNAVIEW to point to the installation directory (e.g. /?/?/?/RNAVIEW)
   Add the following sentences to your shell script.) (or type the two sentences in the window, before executing the program:

   For C shell users:

     setenv RNAVIEW /?/?/?/RNAVIEW

     setenv PATH "/?/?/?/RNAVIEW/bin:"$PATH	

   For Bourne shell users:

     RNAVIEW=/?/?/?/RNAVIEW;  export RNAVIEW 

     PATH="/?/?/?/RNAVIEW/bin:"$PATH; export PATH 

4. To test the program, go to /?/?/?/RNAVIEW/test
   type   rnaview -p tr0001.pdb
   The 2D structure is shown by tr0001.pdb.ps and base pair types is given by tr0001.pdb.out

How to use the program:

Please refer to the README file located in the package (RNAVIEW.tar.gz) , or type

  rnaview -h