Searching and indexing genomic databases via kernelization

被引：17
|
作者：
Gagie, Travis [1 ]
Puglisi, Simon J.
机构：
[1] Univ Helsinki, Dept Comp Sci, POB 68,Gustaf Hallstromin Katu 2b, FI-00014 Helsinki, Finland
来源：
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY | 2015年 / 3卷
基金：
芬兰科学院;
关键词：
approximate pattern matching; data compression; genomic databases; indexing; kernelization; random-access reading; string algorithms;
D O I：
10.3389/fbioe.2015.00012
中图分类号：
Q81 [生物工程学（生物技术）]; Q93 [微生物学];
学科分类号：
071005 ; 0836 ; 090102 ; 100705 ;
摘要：
The rapid advance of DNA sequencing technologies has yielded databases of thousands of genomes. To search and index these databases effectively, it is important that we take advantage of the similarity between those genomes. Several authors have recently suggested searching or indexing only one reference genome and the parts of the other genomes where they differ. In this paper, we survey the 20-year history of this idea and discuss its relation to kernelization in parameterized complexity.
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页数：4
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