Related papers: Statistical Analysis of Hairpins and BasePairs in …
By performing a comprehensive study on 1832 segments of 1212 complete genomes of viruses, we show that in viral genomes the hairpin structures of thermodynamically predicted RNA secondary structures are more abundant than expected under a…
A quantitative characterization of the relationship between molecular sequence and structure is essential to improve our understanding of how function emerges. This particular genotype-phenotype map has been often studied in the context of…
The statistical mechanics of heteropolymer structure formation is studied in the context of RNA secondary structures. A designed RNA sequence biased energetically towards a particular native structure (a hairpin) is used to study the…
A growing number of RNA sequences are now known to have distributions of multiple stable sequences. Recent algorithms use the list of nucleotides in a sequence and auxiliary experimental data to predict such distributions. Although the…
It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution. Hence, prediction of conserved secondary structures from…
We modify and extend the recently developed statistical mechanical model for predicting the thermodynamic properties of chain molecules having noncovalent double-stranded conformations, as in RNA or ssDNA, and $\beta-$sheets in protein, by…
It is a classical result of Stein and Waterman that the asymptotic number of RNA secondary structures is $1.104366 n^{-3/2} 2.618034^n$. In this paper, we study combinatorial asymptotics for two special subclasses of RNA secondary…
Given an RNA sequence a, consider the network G = (V;E), where the set V of nodes consists of all secondary structures of a, and whose edge set E consists of all edges connecting two secondary structures whose base pair distance is 1.…
In this paper we compute the limit distributions of the numbers of hairpin-loops, interior-loops and bulges in k-noncrossing RNA structures. The latter are coarse grained RNA structures allowing for cross-serial interactions, subject to the…
An endhered (end-adhered) pattern is a subset of arcs in matchings, such that the corresponding starting points are consecutive and the same holds for the ending points. Such patterns are in one-to-one correspondence with the permutations.…
In this paper, some statistical distributions of wide pairs included in Double Star Catalogue are investigated. Frequency distributions and testing hypothesis are derived for some basic parameters of visual binaries. The results reached…
Given a random RNA secondary structure, $S$, we study RNA sequences having fixed ratios of nuclotides that are compatible with $S$. We perform this analysis for RNA secondary structures subject to various base pairing rules and minimum arc-…
RNA folding is a kinetic process governed by the competition of a large number of structures stabilized by the transient formation of base pairs that may induce complex folding pathways and the formation of misfolded structures. Despite of…
An RNA sequence is a word over an alphabet on four elements $\{A,C,G,U\}$ called bases. RNA sequences fold into secondary structures where some bases match one another while others remain unpaired. Pseudoknot-free secondary structures can…
The ensemble of RNA secondary structures of uniform sequences is studied analytically. We calculate the partition function for very long sequences and discuss how the cross-over length, beyond which asymptotic scaling laws apply, depends on…
Combinatorial analysis of a certain abstract of RNA structures has been studied to investigate their statistics. Our approach regards the backbone of secondary structures as an alternate sequence of paired and unpaired sets of nucleotides,…
The effect of secondary structure on DNA duplex formation is poorly understood. We use a coarse-grained model of DNA to show that specific 3- and 4-base pair hairpins reduce hybridization rates by factors of 2 and 10 respectively, in good…
The primary structure of a ribonucleic acid (RNA) molecule can be represented as a sequence of nucleotides (bases) over the alphabet {A, C, G, U}. The secondary or tertiary structure of an RNA is a set of base pairs which form bonds between…
Formation of base pairs between the nucleotides of an RNA sequence gives rise to a complex and often highly branched RNA structure. While numerous studies have demonstrated the functional importance of the high degree of RNA branching --…
In this paper, we use the biological domain knowledge incorporated into stochastic models for ab initio RNA secondary-structure prediction to improve the state of the art in joint compression of RNA sequence and structure data (Liu et al.,…