Introduction:

DiscoverR is a software tool for discovering common patterns from two RNA secondary structures. The program is written in Java.

Download:   DiscoverR.jar

Installation:

1.  Download DiscoverR.jar.

2.  Extract DiscoverR.jar to your installation directory by typing

       jar xf DiscoverR.jar

3.  A directory named "DiscoverR" will appear. Switch to it by typing

      cd DiscoverR

Instructions:

Type

java discoverr/DiscoverR -d qRNA.struct dRNA.struct -x 0.1

The above command finds the common patters of the query RNA secondary structure stored in the input file named qRNA.struct and the subject RNA secondary structure stored in the input file named dRNA.struct.

-x specifies the dissimilarity threshold used by the program; the threshold value here is 0.1.

In the input file qRNA.struct (dRNA.struct, respectively), the query (subject, respectively) RNA secondary structure is represented using the Vienna style dot-parenthesis notation. Each input file has three lines: header line, primary sequence line and structure notation line. (Sample: qRNA.struct, dRNA.struct.)

The output file contains the common patterns found in the query RNA secondary structure stored in the file qRNA.struct and the subject RNA secondary structure stored in the file dRNA.struct. Each pattern structure is represented using the Vienna style dot-parenthesis notation. The beginning position and the ending position of each contiguous subsequence in each pattern are highlighted. (Sample: result.) Click here to see the graphical display of the common patterns found in the sample RNA secondary structures portrayed using RNAViz.

For any suggestions, comments or queries about this website, please contact jason.t.wang@njit.edu.