A Comparison of DNA Fragment Assembly Algorithms

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.

• Type: Conference
• Year: 2004
• Where: METMBS
• Authors: Lishan Li, Sami Khuri
• Keywords: DNA Fragment Assembly, Fragment Assembly Problem, Mathematics, METMBS 2004, Sequencing