Add Nussinov Algorithm for RNA Secondary Structure Prediction #6071
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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
BamaCharanChhandogi,
alxkm,
siriak,
vil02 and
yanglbme
as code owners
siriak
requested changes
Nov 1, 2024
|
It would be best if you stopped posting comments without sense. |
|
This pull request has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contribution! |
|
Please reopen this pull request once you have made the required changes. If you need help, feel free to ask in our Discord server or ping one of the maintainers here. Thank you for your contribution! |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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.