Angela’s collaborative manuscript with the Bagheri lab,“DUETT quantitatively identifies known and novel events in nascent RNA structural dynamics from chemical probing data,” is now published in Bioinformatics!
Detection of Unknown Events with Tunable Thresholds (DUETT) enables fast, systematic, and quantitative detection of cotranscriptional SHAPE-Seq reactivity changes, which only had been done by human visualization. The method is inspired by proportional-integral feedback control and linear regression to detect both sudden and gradual changes in reactivity. We applied DUETT to the E. coli signal recognition particle (SRP) RNA and the B. cereus crcB fluoride riboswitch and found new and previously noted events in cotranscriptional SHAPE-Seq data, reflecting RNA structural changes during transcription. DUETT will thus enable rapid identification of events difficult to detect by manual identification in cotranscriptional SHAPE-Seq data!