|Title:||Evaluation of Transat by comparing it to other co-transcriptional software|
Department of Computer Science, University of British Columbia
RNA folding and transcription are not separate processes in vivo. Transcribed RNA sequences can begin folding before transcription is terminated. These temporary structures can be destroyed and reformed according to transcriptional speed, further sequences and ironic environments etc. RNA "co-transcription folding" is used to describe such phenomenon. One hypothesis is that the transient helices formed during transcription can be structural conserved under evolution to maintain the folding pathway that finally leads to the stable functional structure (Meyer and Nick). To test the hypothesis, Transat is developed and is used to identify evolutionarily conserved RNA helices that have statistically significance. However, Transat itself does not simulate the folding pathway itself. My rotation work is to evaluate the performance of Transat by comparing it to other state-of-art software (Kinetics, Kinwalker, RNAKinetics) that simulate RNA co-transcriptional folding. Currently, 16 bacteria alignments have been tested.