External memory approach to compute the maximal repeats across classes from DNA sequences

ASIAIR > College of Computer Science > Department of Computer Science and Information Engineering > Journal Artical > Item 310904400/8955

Please use this identifier to cite or link to this item: http://asiair.asia.edu.tw/ir/handle/310904400/8955

Title:	External memory approach to compute the maximal repeats across classes from DNA sequences
Authors:	Jing-Doo Wang
Keywords:	maximal repeat;external memory;genomic comparison
Date:	2006
Issue Date:	2010-04-15 05:42:24 (UTC+0)
Abstract:	This work presents an external memory approach to extract the maximal repeats from whole genome sequences with the statistics of these repeats across classes, where the definition of a class is determined from the statistics to be computed. A heuristic method consisting of a bucket-sort-like approach and the Chinese term extraction approach is adopted. The bucket-sorting method is used to sort the suffixes of DNA sequences stored in files, and the term extraction is used to extract maximal repeats by scanning the sorted suffixes while computing the statistics of these repeats. The statistics of these repeats across classes might be useful for sequence classification and species identification.
Relation:	Asian Journal of Health and Information Sciences 1(3) : 276-295
Appears in Collections:	[Department of Computer Science and Information Engineering] Journal Artical

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