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RNA Secondary Structure Prediction

CSE 549 - Computational Biology                                                                                                                                                                                                   Home       Back to Courses 
Team: Nicolo Davis, Sagnik Dhar, Ritin M Suthagaran

RNA Secondary structure analysis is a problem which computer scientists have tried to solve using computational techniques like Dynamic Programming and similar Greedy approaches. In this project, we have tried to analyze how well a Simulated Annealing approach would solve the problem of finding a structure which corresponds to a global minimum free energy value. This would correspond to the most stable structural state of a particular RNA sequence and is hence biologically important. After our previous update report (attached), we have gone ahead and improved the Simulated Annealing(SA) algorithm and the Rank() function. In our previous SA approach, codons were replaced by equivalent codons. Now we also take into consideration, the possibility of a codon being swapped with another codon present in the same sequence as this has a high biological possibility. The Rank() function calculates the Energy of an RNA sequence. We have made the Energy calculation more accurate by detecting more structural properties than before and taking into account the energy contributions of those. We have tested our algorithm on 5 RNA sequences and compared our results with a standard
dynamic programming-based algorithm called UNAFold.

- Project update report
- Final project report

- Source code
(Disclaimer: All code provided here is on a "as is" basis. I do not take responsibility for the effect this code has on your machine. All code has been tested prior to its upload. However, it's not been tested exhaustively. Use at your own desire.)

Sagnik Dhar,
Jan 29, 2010, 8:14 PM
Sagnik Dhar,
Jan 29, 2010, 8:14 PM
Sagnik Dhar,
Jan 29, 2010, 8:13 PM