Research Article
Evidence of higher order patterns in information transmission between nucleotide sequences and folded molecular shapes of RNA
@INPROCEEDINGS{10.4108/eai.3-12-2015.2262552, author={Christopher Barrett and Fenix Huang and Christian Reidys}, title={Evidence of higher order patterns in information transmission between nucleotide sequences and folded molecular shapes of RNA}, proceedings={9th EAI International Conference on Bio-inspired Information and Communications Technologies (formerly BIONETICS)}, publisher={ACM}, proceedings_a={BICT}, year={2016}, month={5}, keywords={rna sequence-structure relation partition function boltzmann sampling entropy}, doi={10.4108/eai.3-12-2015.2262552} }- Christopher Barrett
Fenix Huang
Christian Reidys
Year: 2016
Evidence of higher order patterns in information transmission between nucleotide sequences and folded molecular shapes of RNA
BICT
EAI
DOI: 10.4108/eai.3-12-2015.2262552
Abstract
This contribution is a short version of a full paper submitted to Bioinformatics. DNA data transcribe into single stranded RNA, which folds into specific configurations. On the level of contact structures these are described by RNA secondary structures. Here we stipulate that RNA structures provide semantics for sequential DNA data. Accordingly we study the correlation between RNA sequences and RNA structures. We compute the partition function of sequences with respect to a fixed structure. We present a Boltzmann sampler and obtain the a priori probability of specific sequence patterns in such samples. We present a detailed analysis for the two PDB-structures, 2JXV (hairpin) and 2N3R (3-branch multi-loop). We localize where specific sequence patterns occur, contrast the energy spectrum of Boltzmann sampled sequences versus those sequences that refold into the same structure and derive a criterion to identify native structures.