SimTree 

Computing similarity between RNA secondary structure

The SimTree server receives two RNA secondary structures in parentheses representation. It returns a similarity score and a mapping between the similar regions of the two structures.
Running example Usage instructions SimTree paper Supplementary material

Sequence 1:
Insert a RNA secondary structure in parentheses representation, or a RNA primary sequence in a FASTA format.
Input type: Parentheses FASTA
Paste the data into the field below:

Sequence 2:
Insert a RNA secondary structure in parentheses representation, or a RNA primary sequence in a FASTA format.
Input type: Parentheses FASTA
Paste the data into the field below:

Note: when inserting the RNA sequence in FASTA format the SimTree server uses the RNAfold module from the RNA Vienna Package in order to predict secondary structures.
Parameters:

Details (returns the property of each node in each tree in a pre-order traversal).

Mapping (returns the mapping of the nodes between the two trees).

Use  flip operations.

Note: a sequence length for an online submission is limited to 500 bases. In order to process logner jobs, please download the application for an offline use.

Download SimTree_v1.2.3

SimTree is written in Java and supplied as a Java Archive file (JAR). Thus, one needs the Java Run-Time Environment (JRE) installed in order to use it. You can get it at http://www.java.sun.com.
Note that the JRE has a default memory size limitation of 64Mb per process. Thus, in order to analyze large structures use the '-Xmx' flag to define a higher limit:
`java -Xmx512m -jar SimTree.jar`
(in the above example '-Xmx' defines a new limitation of 512Mb instead of the default 64Mb).

Comments, suggestions and bugs may be reported to izharw@keddem.com