An Efficient Genome Fragment Assembling Using GA with Neighborhood Aware Fitness Function
Joint Authors
Chakraborty, Goutam
Kikuchi, Satoko
Source
Applied Computational Intelligence and Soft Computing
Issue
Vol. 2012, Issue 2012 (31 Dec. 2012), pp.1-11, 11 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2012-07-08
Country of Publication
Egypt
No. of Pages
11
Main Subjects
Information Technology and Computer Science
Abstract EN
To decode a long genome sequence, shotgun sequencing is the state-of-the-art technique.
It needs to properly sequence a very large number, sometimes as large as millions, of short partially readable strings (fragments).
Arranging those fragments in correct sequence is known as fragment assembling, which is an NP-problem.
Presently used methods require enormous computational cost.
In this work, we have shown how our modified genetic algorithm (GA) could solve this problem efficiently.
In the proposed GA, the length of the chromosome, which represents the volume of the search space, is reduced with advancing generations, and thereby improves search efficiency.
We also introduced a greedy mutation, by swapping nearby fragments using some heuristics, to improve the fitness of chromosomes.
We compared results with Parsons’ algorithm which is based on GA too.
We used fragments with partial reads on both sides, mimicking fragments in real genome assembling process.
In Parsons’ work base-pair array of the whole fragment is known.
Even then, we could obtain much better results, and we succeeded in restructuring contigs covering 100% of the genome sequences.
American Psychological Association (APA)
Kikuchi, Satoko& Chakraborty, Goutam. 2012. An Efficient Genome Fragment Assembling Using GA with Neighborhood Aware Fitness Function. Applied Computational Intelligence and Soft Computing،Vol. 2012, no. 2012, pp.1-11.
https://search.emarefa.net/detail/BIM-510291
Modern Language Association (MLA)
Kikuchi, Satoko& Chakraborty, Goutam. An Efficient Genome Fragment Assembling Using GA with Neighborhood Aware Fitness Function. Applied Computational Intelligence and Soft Computing No. 2012 (2012), pp.1-11.
https://search.emarefa.net/detail/BIM-510291
American Medical Association (AMA)
Kikuchi, Satoko& Chakraborty, Goutam. An Efficient Genome Fragment Assembling Using GA with Neighborhood Aware Fitness Function. Applied Computational Intelligence and Soft Computing. 2012. Vol. 2012, no. 2012, pp.1-11.
https://search.emarefa.net/detail/BIM-510291
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-510291