Searching and Indexing Genomic Databases via Kernelization

Searching and Indexing Genomic Databases via Kernelization

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 re...

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Bibliographic Details
Main Authors: Travis eGagie, Simon ePuglisi
Format: Article
Language:English
Published: Frontiers Media S.A. 2015-02-01
Series:Frontiers in Bioengineering and Biotechnology
Subjects:
Data Compression
Kernelization
String algorithms
Indexes
Approximate pattern matching
genomic databases
Online Access:http://journal.frontiersin.org/Journal/10.3389/fbioe.2015.00012/full
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spelling doaj-0754ef4c8d774918b646584405640cde2020-11-25T01:51:03ZengFrontiers Media S.A.Frontiers in Bioengineering and Biotechnology2296-41852015-02-01310.3389/fbioe.2015.00012129947Searching and Indexing Genomic Databases via KernelizationTravis eGagie0Simon ePuglisi1University of HelsinkiUniversity of HelsinkiThe 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 twenty-year history of this idea and discuss its relation to kernelization in parameterized complexity.http://journal.frontiersin.org/Journal/10.3389/fbioe.2015.00012/fullData CompressionKernelizationString algorithmsIndexesApproximate pattern matchinggenomic databases
collection DOAJ
language English
format Article
sources DOAJ
author Travis eGagie
Simon ePuglisi
spellingShingle Travis eGagie
Simon ePuglisi
Searching and Indexing Genomic Databases via Kernelization
Frontiers in Bioengineering and Biotechnology
Data Compression
Kernelization
String algorithms
Indexes
Approximate pattern matching
genomic databases
author_facet Travis eGagie
Simon ePuglisi
author_sort Travis eGagie
title Searching and Indexing Genomic Databases via Kernelization
title_short Searching and Indexing Genomic Databases via Kernelization
title_full Searching and Indexing Genomic Databases via Kernelization
title_fullStr Searching and Indexing Genomic Databases via Kernelization
title_full_unstemmed Searching and Indexing Genomic Databases via Kernelization
title_sort searching and indexing genomic databases via kernelization
publisher Frontiers Media S.A.
series Frontiers in Bioengineering and Biotechnology
issn 2296-4185
publishDate 2015-02-01
description 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 twenty-year history of this idea and discuss its relation to kernelization in parameterized complexity.
topic Data Compression
Kernelization
String algorithms
Indexes
Approximate pattern matching
genomic databases
url http://journal.frontiersin.org/Journal/10.3389/fbioe.2015.00012/full
work_keys_str_mv AT travisegagie searchingandindexinggenomicdatabasesviakernelization
AT simonepuglisi searchingandindexinggenomicdatabasesviakernelization
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