Add Nussinov Algorithm for RNA Secondary Structure Prediction #6071
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Initial commit: Implemented Nussinov algorithm for RNA secondary structure prediction - Added main class `Nussinov` for RNA secondary structure prediction using dynamic programming. - Implemented base pair compatibility checks and dynamic programming matrix setup. - Included support for reconstructing the RNA folding structure. - Added evaluation function to score the correctness of RNA folding predictions. This implementation aims to maximize base-pair compatibility in RNA sequences.
Add link to the library
alexcerezo
requested review from
yanglbme,
vil02,
BamaCharanChhandogi,
alxkm and
siriak
as code owners
siriak
requested changes
Nov 1, 2024
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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:
Nussinovclass: Implements the Nussinov algorithm with methods for:estRNAFoldingFiles Added:
Nussinov.java: Contains the main algorithm.TestRNAFolding.java: Includes unit tests to verify functionality and accuracy.Additional Notes:
Testing:
All tests included in
TestRNAFoldinghave 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.