Parallel hierarchical adaptive genetic algorithm for fragment assembly

Author

Kim, Kieun ; Mohan, Chilnkuri K.

Author_Institution

Dept. of EECS, Syracuse Univ., NY, USA

Volume

1

fYear

2003

fDate

8-12 Dec. 2003

Firstpage

600

Abstract

Fragment assembly is an important task in genome sequencing, and involves reconstructing a long sequence based on many overlapping subsequences (fragments) that contain errors. This paper presents a fragment assembler using a new parallel hierarchical adaptive variation of evolutionary algorithms. The innovative features include a new measure for evaluating sequence assembly quality and the development of a hybrid algorithm. Results from the simulation of 56 cases demonstrate that sequence assembly by the new sequencing method is highly accurate and noise-tolerant.

Keywords

DNA; adaptive systems; genetic algorithms; genetics; molecular configurations; parallel algorithms; sequences; adaptive genetic algorithm; evolutionary algorithms; fragment assembly; genome sequencing; hierarchical genetic algorithm; hybrid algorithm development; overlapping subsequences; parallel genetic algorithm; sequence assembly quality; sequence reconstruction; sequencing method; Assembly; Bioinformatics; Cloning; DNA; Evolutionary computation; Genetic algorithms; Genomics; Probes; Sequences; Technological innovation;

fLanguage

English

Publisher

ieee

Conference_Titel

Evolutionary Computation, 2003. CEC '03. The 2003 Congress on

Print_ISBN

0-7803-7804-0

Type

conf

DOI

10.1109/CEC.2003.1299631

Filename

1299631