This mini-project was implemented as a part of UGA's CSCI 6470 Algorithms course.
The aim of this project is to compute the maximum number of permissible letter pairs from the input sequence of 4 letters (A, C, G, U). For these letters, legal pairs are A-U, U-A, G-C, C-G. This problem is called Structure Prediction because it is a meaningful abstraction of the significant problem RNA secondary structure prediction in computational biology. The letters in the input sequence are replaced with denotational symbols '{' and '}' underlining the sequence indicate which two letters are predicted to be paired and the dot symbol ’.’ indicates a letter predicted to be not paired with any other.
For example,
Input: AUGUCAGCGUU
Output: { } { . } { { } . } .
Sean Eddy, How do RNA Folding Algorithms Work? Nature Biotechnology, Vol 22, No. 7, July 2004.
This section describes the preqrequisites, and contains instructions, to get the project up and running.
The user can get a description of the options by using the command: $ python __main__.py --help.
User Options:
- --energy
If True, returns specific gamma-scores for each base- pair. If False, returns 1 for each base-pair.
- --gap
Number of bases between two nucleotide bases in sequence.
- --include_AU
If True, includes A-U base pair in DP-Table formulation.
There are no specific guidelines for contributing, apart from a few general rules such as:
- Code should follow PEP8 standards as closely as possible
- We use Google-Style docstrings to document the Python modules in this project.
If you see something that could be improved, send a pull request!
I am always happy to look at improvements, to ensure that rna-structure-prediction, as a project, is the best version of itself.
If you think something should be done differently (or is just-plain-broken), please create an issue.
See the LICENSE file for more details.