A tissue P system and a DNA microfluidic device for solving the shortest common superstring problem

Ledesma, Lucas; Manrique, Daniel; Rodríguez‐Patón, Alfonso

doi:10.1007/s00500-004-0423-2

Cited by 3 publications

(1 citation statement)

References 17 publications

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“…Ledesma et al described a tissue P system for solving the Shortest Common Superstring Problem in linear time. 21 Ilie and C. Popescu gave an algorithm for computing optimal solutions which is slow in the number of strings but fast (linear) in their total length. 22 López-Rodríguez and Mérida-Casermeiro, investigated the use of artificial neural networks in order to solve the Shortest Common Superstring Problem.…”

Section: Introductionmentioning

confidence: 99%

DNA Directed Model for Shortest Superstring Problem

Liu¹,

Li²,

Xu³

2011

Jnl of Comp & Theo Nano

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DNA is increasingly being used as the engineering material of choice for the construction of nanoscale circuits, structures, and motors. Recent experimental and theoretical advances have produced and tested new methods to obtain large DNA word sets to support virtually any kind of applications. The problem of finding a Shortest Common Supersequence (SCS) of a set of sequences is an important problem with applications in many areas. This problem is NP -hard and has applications in computational biology and data compression. In this paper, we present a graph model of SCS problem. We characterize the shortest superstring as a Hamiltonian path in a directed graph and give a algotirhm for solving large SCS instances of biological sequences in linear time. As a general computational framework, this algorithm can also be applied on more general applications such as text comparison and compression, query optimization and scheduling.

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Section: Introductionmentioning

confidence: 99%