Parallel hierarchical adaptive genetic algorithm for fragment assembly

Kieun Kim; Chilnkuri K. Mohan

doi:10.1109/CEC.2003.1299631

Parallel hierarchical adaptive genetic algorithm for fragment assembly

Kieun Kim, Chilnkuri K. Mohan

Department of Electrical Engineering & Computer Science

Research output: Contribution to conference › Paper › peer-review

17 Scopus citations

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.

Original language	English (US)
Pages	600-607
Number of pages	8
DOIs	https://doi.org/10.1109/CEC.2003.1299631
State	Published - 2003
Event	2003 Congress on Evolutionary Computation, CEC 2003 - Canberra, ACT, Australia Duration: Dec 8 2003 → Dec 12 2003

Other

Other	2003 Congress on Evolutionary Computation, CEC 2003
Country/Territory	Australia
City	Canberra, ACT
Period	12/8/03 → 12/12/03

ASJC Scopus subject areas

Computational Mathematics

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10.1109/CEC.2003.1299631

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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.",

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AB - 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.

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Parallel hierarchical adaptive genetic algorithm for fragment assembly

Abstract

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