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We present a general setting for structure-sequence comparison in a large class of RNA structures that unifies and generalizes a number of recent works on specific families on structures. Our approach is based on tree decomposition of structures and gives rises to a general parameterized algorithm, where the exponential part of the complexity depends on the family of structures. For each of the previously studied families, our algorithm has the same complexity as the specific algorithm that had been given before.
An $h$-queue layout of a graph $G$ consists of a linear order of its vertices and a partition of its edges into $h$ queues, such that no two independent edges of the same queue nest. The minimum $h$ such that $G$ admits an $h$-queue layout is the que
We propose a new topological characterization of RNA secondary structures with pseudoknots based on two topological invariants. Starting from the classic arc-representation of RNA secondary structures, we consider a model that couples both I) the top
In this paper we consider the problem of RNA folding with pseudoknots. We use a graphical representation in which the secondary structures are described by planar diagrams. Pseudoknots are identified as non-planar diagrams. We analyze the non-planar
Motivation: The ability to generate massive amounts of sequencing data continues to overwhelm the processing capability of existing algorithms and compute infrastructures. In this work, we explore the use of hardware/software co-design and hardware a
CovID-19 genetics analysis is critical to determine virus type,virus variant and evaluate vaccines. In this paper, SARS-Cov-2 RNA sequence analysis relative to region or territory is investigated. A uniform framework of sequence SVM model with variou