RateMySplice is an early computational biology project developed to support experimental investigation of 5′ splice site recognition.
The original aim was to identify positions within a DNA sequence where a nucleotide substitution could generate a putative GT splice donor site.
The workflow was designed to:
- search an input DNA sequence for candidate positions;
- generate sequence variants containing a potential GT donor motif;
- extract the local sequence surrounding each candidate site;
- score the resulting putative splice sites;
- rank candidate mutations for experimental testing.
The repository currently contains the original Python prototype used to generate candidate mutated sequences.
A later version of the project incorporated maximum entropy splice site scoring, developed collaboratively, but that implementation is not contained in this repository.
This repository preserves the original prototype as an example of my early computational biology work.
A future redevelopment is planned as a user friendly sequence analysis tool in which researchers could submit a DNA sequence, generate candidate splice site mutations, score them and prioritise mutations for experimental investigation.
legacy/ — original Python prototype from the undergraduate project.
Future development may include:
- user-supplied DNA sequences;
- systematic generation of candidate splice donor mutations;
- splice site strength scoring;
- ranking and visualisation of candidate mutations;
- a simple web based interface;
- documented and reproducible analysis;
- automated tests.
The project originated during my undergraduate research in splice site recognition and experimental manipulation of splicing.