RNA Secondary Structure Prediction

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dc.contributor.author Anderson, Johshua
dc.contributor.author Ash, Andrew
dc.date.accessioned 2011-03-30T18:22:23Z
dc.date.available 2011-03-30T18:22:23Z
dc.date.issued 2010-11-18
dc.identifier.uri http://hdl.handle.net/1853/38335
dc.description A presentation in the Undergraduate Research Kaleidoscope: Library East Commons Performance Space, November 18, 2010. en_US
dc.description Runtime: 06:54 minutes. en_US
dc.description.abstract Our task has been to calculate the probability of any two nucleotides pairing in an RNA molecule. When RNA goes into the cytoplasm of a cell, the RNA folds in on itself to a thermodynamically stable state, since unpaired nucleotides are chemically unstable. We predict this behavior by a couple of dynamic programming algorithms using some statistical methods derived from the physics of ideal gasses. In order to find base pair probabilities we must first find the partition function for all continuous substrings in the strand. The partition function is a measure of the possible combinations of foldings weighted by the stability of these foldings. We will also describe finding the minimum free energy structure, currently implemented in gtfold, and its relation to the partition function via something we have come to call "tropicalization." Both the minimum free energy and the partition function problems are solved in a reasonable (O(n³)) amount of time by dynamic programming algorithms. en_US
dc.format.extent 06:54 minutes
dc.language.iso en_US en
dc.publisher Georgia Institute of Technology en
dc.subject Bioinformatics en
dc.subject Computational biology en
dc.subject RNA en
dc.subject Computer science en
dc.subject Dynamic programming en
dc.title RNA Secondary Structure Prediction en
dc.type Presentation en
dc.type Video en
dc.contributor.corporatename Georgia Institute of Technology. Undergraduate Research Opportunities Program
dc.contributor.corporatename Georgia Institute of Technology. Library and Information Center
dc.contributor.corporatename Georgia Institute of Technology. School of Computer Science
dc.contributor.corporatename Georgia Institute of Technology. School of Biology
dc.description.advisor Christine Heitsch, David A. Bader and Steve Harvey en_US


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