RNA triplet repeats: improved algorithms for structure prediction and interactions
Kimon Boehmer, Sarah J. Berkemer, Sebastian Will, Yann Ponty
TL;DR
This paper introduces improved algorithms for predicting RNA structures and interactions, focusing on triplet repeats in RNA.
Contribution
The paper presents new algorithms for computing MFE and partition functions for RNA and RNA-RNA interactions, improving computational efficiency.
Findings
Improved algorithms for computing MFE and partition function for RNA secondary structures.
A new algorithm for RNA-RNA interactions with improved running time from factorial to exponential.
A polynomial-time algorithm for computing interactions from a base set of RNA strands.
Abstract
RNAs composed of Triplet Repeats (TR) have recently attracted much attention in the field of synthetic biology. We study the mimimum free energy (MFE) secondary structures of such RNAs and give improved algorithms to compute the MFE and the partition function. Furthermore, we study the interaction of multiple RNAs and design a new algorithm for computing MFE and partition function for RNA-RNA interactions, improving the previously known factorial running time to exponential. In the case of TR, we show computational hardness but still obtain a parameterized algorithm. Finally, we propose a polynomial-time algorithm for computing interactions from a base set of RNA strands and conduct experiments on the interaction of TR based on this algorithm. For instance, we study the probability that a base pair is formed between two strands with the same triplet pattern, allowing an assessment of a…
Genes, proteins, chemicals, diseases, species, mutations and cell lines named across the full text — each resolved to its canonical identifier and authoritative record.
Click any figure to enlarge with its caption.
Figure 10
Figure 11
Figure 12
Figure 13
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8
Figure 9
Figure 14
Figure 15
Figure 16
Figure 17
Figure 18
Figure 19
Figure 20Peer Reviews
No public reviews on file for this paper yet. If you reviewed it on a platform where reviews are public (OpenReview, ICLR, NeurIPS, ICML), you can paste yours below so the community can read it here.
Videos
No videos yet. Explain this paper in a talk, walkthrough, or lecture? Add one.
Taxonomy
TopicsRNA and protein synthesis mechanisms · RNA modifications and cancer · RNA Research and Splicing