ﻻ يوجد ملخص باللغة العربية
In this paper we present a selfcontained analysis and description of the novel {it ab initio} folding algorithm {sf cross}, which generates the minimum free energy (mfe), 3-noncrossing, $sigma$-canonical RNA structure. Here an RNA structure is 3-noncrossing if it does not contain more than three mutually crossing arcs and $sigma$-canonical, if each of its stacks has size greater or equal than $sigma$. Our notion of mfe-structure is based on a specific concept of pseudoknots and respective loop-based energy parameters. The algorithm decomposes into three parts: the first is the inductive construction of motifs and shadows, the second is the generation of the skeleta-trees rooted in irreducible shadows and the third is the saturation of skeleta via context dependent dynamic programming routines.
In this paper we study $k$-noncrossing, canonical RNA pseudoknot structures with minimum arc-length $ge 4$. Let ${sf T}_{k,sigma}^{[4]} (n)$ denote the number of these structures. We derive exact enumeration results by computing the generating functi
In this paper we study the distribution of stacks in $k$-noncrossing, $tau$-canonical RNA pseudoknot structures ($<k,tau> $-structures). An RNA structure is called $k$-noncrossing if it has no more than $k-1$ mutually crossing arcs and $tau$-canonica
In this paper we analyze the length-spectrum of blocks in $gamma$-structures. $gamma$-structures are a class of RNA pseudoknot structures that plays a key role in the context of polynomial time RNA folding. A $gamma$-structure is constructed by nesti
In this paper we study $k$-noncrossing RNA structures with minimum arc-length 4 and at most $k-1$ mutually crossing bonds. Let ${sf T}_{k}^{[4]}(n)$ denote the number of $k$-noncrossing RNA structures with arc-length $ge 4$ over $n$ vertices. We prov
In this paper we enumerate $k$-noncrossing RNA pseudoknot structures with given minimum arc- and stack-length. That is, we study the numbers of RNA pseudoknot structures with arc-length $ge 3$, stack-length $ge sigma$ and in which there are at most $