A Comparison of DNA Fragment Assembly Algorithms
نویسندگان
چکیده
As more research centers embark on sequencing new genomes, the problem of DNA fragment assembly for shotgun sequencing is growing in importance and complexity. Accurate and fast assembly is a crucial part of any sequencing project and many algorithms have been developed to tackle it. Since the DNA fragment assembly problem is NP-hard, exact solutions are very difficult to obtain. In this work, we present four heuristic algorithms, which we designed, implemented and tested. We compare the algorithms and the data structures of the four heuristics and present results of our experiments. We also compare our results with the assemblies produced by the wellknown packages: PHRAP and CAP3.
منابع مشابه
Diamondoids and DNA Nanotechnologies
Diamondoids are cage-like saturated hydrocarbons consisting of fused cyclohexane rings. The Diamondoids family of compounds is one of the best candidates for molecular building blocks (MBBs) in nanotechnology to construct organic nanostructures compared to other MBBs known so far. The challenge is to find a route for self-assembly of these cage hydrocarbons and their applications in the bottom-...
متن کاملModified Classical Graph Algorithms for the DNA Fragment Assembly Problem
DNA fragment assembly represents an important challenge to the development of efficient and practical algorithms due to the large number of elements to be assembled. In this study, we present some graph theoretical linear time algorithms to solve the problem. To achieve linear time complexity, a heap with constant time operations was developed, for the special case where the edge weights are in...
متن کاملAssembling DNA Fragments with a Distributed Genetic Algorithm
As more research centers embark on sequencing new genomes, the problem of DNA fragment assembly for shotgun sequencing is growing in importance and complexity. Accurate and fast assembly is a crucial part of any sequencing project and many algorithms have been developed to tackle it. Since the DNA fragment assembly problem is NP-hard, exact solutions are very difficult to obtain. Various heuris...
متن کاملDNA Fragment Assembly Using Multi-Objective Genetic Algorithms
DNA Fragment Assembly Problem (FAP) is concerned with the reconstruction of the target DNA, using the several hundreds (or thousands) of sequenced fragments, by identifying the right order and orientation of each fragment in the layout. Several algorithms have been proposed for solving FAP. Most of these have solely dwelt on the single objective of maximizing the sum of the overlaps between adj...
متن کاملSolving a multi-objective mixed-model assembly line balancing and sequencing problem
This research addresses the mixed-model assembly line (MMAL) by considering various constraints. In MMALs, several types of products which their similarity is so high are made on an assembly line. As a consequence, it is possible to assemble and make several types of products simultaneously without spending any additional time. The proposed multi-objective model considers the balancing and sequ...
متن کامل