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 refe...

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Detalles Bibliográficos
Autores principales: Gagie, Travis, Puglisi, Simon J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2015
Materias:
Bioengineering and Biotechnology
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4321636/
https://www.ncbi.nlm.nih.gov/pubmed/25710001
http://dx.doi.org/10.3389/fbioe.2015.00012
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author Gagie, Travis
Puglisi, Simon J.
author_facet Gagie, Travis
Puglisi, Simon J.
author_sort Gagie, Travis
collection PubMed
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 20-year history of this idea and discuss its relation to kernelization in parameterized complexity.
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spelling pubmed-43216362015-02-23 Searching and Indexing Genomic Databases via Kernelization Gagie, Travis Puglisi, Simon J. Front Bioeng Biotechnol Bioengineering and Biotechnology 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. Frontiers Media S.A. 2015-02-09 /pmc/articles/PMC4321636/ /pubmed/25710001 http://dx.doi.org/10.3389/fbioe.2015.00012 Text en Copyright © 2015 Gagie and Puglisi. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Bioengineering and Biotechnology
Gagie, Travis
Puglisi, Simon J.
Searching and Indexing Genomic Databases via Kernelization
title 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_short Searching and Indexing Genomic Databases via Kernelization
title_sort searching and indexing genomic databases via kernelization
topic Bioengineering and Biotechnology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4321636/
https://www.ncbi.nlm.nih.gov/pubmed/25710001
http://dx.doi.org/10.3389/fbioe.2015.00012
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