Add Nussinov Algorithm for RNA Secondary Structure Prediction

[alexcerezo]

Description: This pull request introduces the implementation of the Nussinov algorithm, which predicts the secondary structure of RNA by maximizing base-pair compatibility. The algorithm uses dynamic programming to compute an optimal structure based on RNA sequence input.

Changes:

• Added Nussinov class: Implements the Nussinov algorithm with methods for:
  • Checking base-pair compatibility.
  • Constructing the dynamic programming matrix to predict secondary structures.
  • Reconstructing the optimal folding structure from the computed matrix.
  • Evaluating the accuracy of predictions based on paired bases.
• Test file: estRNAFolding
  • Tests base-pair compatibility with various pairs.
  • Verifies correct secondary structure prediction for short RNA sequences.

Files Added:

1. Nussinov.java: Contains the main algorithm.
2. TestRNAFolding.java: Includes unit tests to verify functionality and accuracy.

Additional Notes:

• The implementation follows standard dynamic programming principles and is optimized for clarity.
• Future improvements could involve more complex test cases and compatibility with additional nucleotide pairs.

Testing: All tests included in TestRNAFolding have been successfully run, covering both base-pair compatibility and basic structure prediction. A library it needed, link on the Nussinov.java file.

This addition should be a valuable resource for bioinformatics and computational biology algorithms in the repository.