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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




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