Running example:

 

Input:

 

Sequence1:

(((((((..((((.........))))...(((..(((...)))..))).(((((.......))))))))))))

 

Sequence2:

(((((((................((.(((((((.......))))))).))(((((.......))))))))))))

 

 

Output

 

T1  --> T2

-------------

0 --> null

1 --> 1

2 --> 2

3 --> null

4 --> null

5 --> 3

6 --> 4

7 --> 5

8 --> 6

9 --> 7

10 --> 8

 

Complexity of T1: 10

Complexity of T2: 8

Score: 7.2812

Normalized Score: 0.8140

 

 

Interpretation of results:

 

Score: similarity score between the two secondary structures. A high score indicates high similarity. The values of the score range between 0 and the size of the smaller tree.

 

Normalized Score: is the normalized score after taking into account the tree sizes. The values of the normalized score are between 0 and 1 where 1 indicates a perfect match.

In cases where the structures that are compared vary in sizes it is recommended to use the normalized score instead of the score.

 

Mapping: Specifies the matching substructures between the first and the second structures. In the above running example Sequence1 and Sequnce2 correspond to the tRNA structures shown in the figure below. The mapping specifies which of the substructures are matching.

4

 

(b)

tRNA II - secondary structure with the nodes numbered according to their preorder traversal

 

 

(a)

tRNA I - secondary structure with the nodes numbered according to their preorder traversal

 

3

 

7

 

8

 

6

 

5

 

2

 

1

 

10

 

9

 

8

 

7

 

6

 

5

 

4

 

3

 

1

 

2