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dc.contributor.authorAnderson, Johshua
dc.contributor.authorAsh, Andrew
dc.date.accessioned2011-03-30T18:22:23Z
dc.date.available2011-03-30T18:22:23Z
dc.date.issued2010-11-18
dc.identifier.urihttp://hdl.handle.net/1853/38335
dc.descriptionA presentation in the Undergraduate Research Kaleidoscope: Library East Commons Performance Space, November 18, 2010.en_US
dc.descriptionRuntime: 06:54 minutes.en_US
dc.description.abstractOur 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.extent06:54 minutes
dc.language.isoen_USen
dc.publisherGeorgia Institute of Technologyen
dc.subjectBioinformaticsen
dc.subjectComputational biologyen
dc.subjectRNAen
dc.subjectComputer scienceen
dc.subjectDynamic programmingen
dc.titleRNA Secondary Structure Predictionen
dc.typePresentationen
dc.typeVideoen
dc.contributor.corporatenameGeorgia Institute of Technology. Undergraduate Research Opportunities Program
dc.contributor.corporatenameGeorgia Institute of Technology. Library and Information Center
dc.contributor.corporatenameGeorgia Institute of Technology. School of Computer Science
dc.contributor.corporatenameGeorgia Institute of Technology. School of Biology
dc.description.advisorChristine Heitsch, David A. Bader and Steve Harveyen_US


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