Search arXiv⌕ Search
Home/Archive/arXiv

arXiv · 0905.0733

Inverse folding of RNA pseudoknot structures

James Z. M. Gao·Linda Y. M. Li·Christian M. Reidys
View original source ↗Read source document ↗Export metadata ↓

Abstract

Background: RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and \pairGU-base pairings (secondary structure) and additional cross-serial base pairs. These interactions are called pseudoknots and are observed across the whole spectrum of RNA functionalities. In the context of studying natural RNA structures, searching for new ribozymes and designing artificial RNA, it is of interest to find RNA sequences folding into a specific structure and to analyze their induced neutral networks. Since the established inverse folding algorithms, {\tt RNAinverse}, {\tt RNA-SSD} as well as {\tt INFO-RNA} are limited to RNA secondary structures, we present in this paper the inverse folding algorithm {\tt Inv} which can deal with 3-noncrossing, canonical pseudoknot structures. Results: In this paper we present the inverse folding algorithm {\tt Inv}. We give a detailed analysis of {\tt Inv}, including pseudocodes. We show that {\tt Inv} allows to design in particular 3-noncrossing nonplanar RNA pseudoknot 3-noncrossing RNA structures-a class which is difficult to construct via dynamic programming routines. {\tt Inv} is freely available at \url{http://www.combinatorics.cn/cbpc/inv.html}. Conclusions: The algorithm {\tt Inv} extends inverse folding capabilities to RNA pseudoknot structures. In comparison with {\tt RNAinverse} it uses new ideas, for instance by considering sets of competing structures. As a result, {\tt Inv} is not only able to find novel sequences even for RNA secondary structures, it does so in the context of competing structures that potentially exhibit cross-serial interactions.

Explore related subjects

math.COq-bio.QM

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

James Z. M. Gao, Linda Y. M. Li, Christian M. Reidys. 2010-03-11. Inverse folding of RNA pseudoknot structures. https://arxiv.org/abs/0905.0733

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

Orthogonal Pairs in Maps from the Sphere to the Circle

We prove that, for any $f:S^2\to S^1$ and any $\varepsilon>0$, there exist orthogonal vectors $x,y\in S^2$ such that the length of the shortest arc between $f(x)$ and $f(y)$ is at most $π/2 +\varepsilon$. This proves a conjecture of Ghebleh from 2007 that the circular chromatic number of the real orthogonality graph is equal to four.

math.CO↗
arXiv2026

Exact Area-Range Minima in the Quantitative Monsky Problem for Five and Seven Triangles

For a dissection $D$ of the unit square into $n$ nondegenerate triangles, let $R(D)=\max_i a_i-\min_i a_i, Δ(n)=\inf_D R(D).$ We prove that this infimum is attained for every $n\ge2$, and determine the exact minima for $n=5$ and $n=7$, allowing T-junctions. For five triangles, $Δ(5)=\frac{5\sqrt5-11}{8};$ equality holds precisely when three areas equal $(3-\sqrt5)/4$ and two equal $(3\sqrt5-5)/8$. For seven triangles, $Δ(7)=r_7$, where $r_7$ is the unique root in $(0,1/4900)$ of $864r^4+2160r^3-6060r^2+4972r-1.$ Every minimizer has four areas $(1+3r_7)/7$ and three areas $(1-4r_7)/7$, although its geometry need not be unique. The proofs combine finite combinatorial classification with exact symbolic and integer-interval certificates. For nine triangles, a tilted-strip construction gives the explicit algebraic upper bound $Δ(9)\le 0.0001273496861283553341\ldots,$ which is the exact minimum within that topology. Conversely, every dissection in the complete single-cap two-rail zig-zag family, with arbitrary continuous areas, has range greater than $1/3500$; hence a global minimizer must lie outside that family. The exact value of $Δ(9)$ remains open.

math.CO↗
arXiv2026

Chromatic symmetric functions for annular webs

We introduce a combinatorial definition of chromatic symmetric functions for annular webs. We prove their symmetry by constructing a web analogue of the Shareshian--Wachs involution and show that they coincide with the symmetric functions associated to annular webs via Turaev's isomorphism. We then derive explicit formulas for their hook Schur coefficients. We also introduce web LLT functions, whose hook Schur coefficients admit positive Laurent-polynomial formulas. These formulas yield a combinatorial expression for the coefficients of the HOMFLY--PT polynomial of an annular web.

math.CO↗