Databases of the marine metagenomics

Handle URI:
http://hdl.handle.net/10754/581767
Title:
Databases of the marine metagenomics
Authors:
Mineta, Katsuhiko ( 0000-0002-4727-045X ) ; Gojobori, Takashi ( 0000-0001-7850-1743 )
Abstract:
The metagenomic data obtained from marine environments is significantly useful for understanding marine microbial communities. In comparison with the conventional amplicon-based approach of metagenomics, the recent shotgun sequencing-based approach has become a powerful tool that provides an efficient way of grasping a diversity of the entire microbial community at a sampling point in the sea. However, this approach accelerates accumulation of the metagenome data as well as increase of data complexity. Moreover, when metagenomic approach is used for monitoring a time change of marine environments at multiple locations of the seawater, accumulation of metagenomics data will become tremendous with an enormous speed. Because this kind of situation has started becoming of reality at many marine research institutions and stations all over the world, it looks obvious that the data management and analysis will be confronted by the so-called Big Data issues such as how the database can be constructed in an efficient way and how useful knowledge should be extracted from a vast amount of the data. In this review, we summarize the outline of all the major databases of marine metagenome that are currently publically available, noting that database exclusively on marine metagenome is none but the number of metagenome databases including marine metagenome data are six, unexpectedly still small. We also extend our explanation to the databases, as reference database we call, that will be useful for constructing a marine metagenome database as well as complementing important information with the database. Then, we would point out a number of challenges to be conquered in constructing the marine metagenome database.
KAUST Department:
Computational Bioscience Research Center (CBRC)
Citation:
Databases of the marine metagenomics 2015 Gene
Publisher:
Elsevier BV
Journal:
Gene
Issue Date:
28-Oct-2015
DOI:
10.1016/j.gene.2015.10.035
Type:
Article
ISSN:
03781119
Additional Links:
http://linkinghub.elsevier.com/retrieve/pii/S0378111915012433
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC)

Full metadata record

DC FieldValue Language
dc.contributor.authorMineta, Katsuhikoen
dc.contributor.authorGojobori, Takashien
dc.date.accessioned2015-11-05T06:24:18Zen
dc.date.available2015-11-05T06:24:18Zen
dc.date.issued2015-10-28en
dc.identifier.citationDatabases of the marine metagenomics 2015 Geneen
dc.identifier.issn03781119en
dc.identifier.doi10.1016/j.gene.2015.10.035en
dc.identifier.urihttp://hdl.handle.net/10754/581767en
dc.description.abstractThe metagenomic data obtained from marine environments is significantly useful for understanding marine microbial communities. In comparison with the conventional amplicon-based approach of metagenomics, the recent shotgun sequencing-based approach has become a powerful tool that provides an efficient way of grasping a diversity of the entire microbial community at a sampling point in the sea. However, this approach accelerates accumulation of the metagenome data as well as increase of data complexity. Moreover, when metagenomic approach is used for monitoring a time change of marine environments at multiple locations of the seawater, accumulation of metagenomics data will become tremendous with an enormous speed. Because this kind of situation has started becoming of reality at many marine research institutions and stations all over the world, it looks obvious that the data management and analysis will be confronted by the so-called Big Data issues such as how the database can be constructed in an efficient way and how useful knowledge should be extracted from a vast amount of the data. In this review, we summarize the outline of all the major databases of marine metagenome that are currently publically available, noting that database exclusively on marine metagenome is none but the number of metagenome databases including marine metagenome data are six, unexpectedly still small. We also extend our explanation to the databases, as reference database we call, that will be useful for constructing a marine metagenome database as well as complementing important information with the database. Then, we would point out a number of challenges to be conquered in constructing the marine metagenome database.en
dc.language.isoenen
dc.publisherElsevier BVen
dc.relation.urlhttp://linkinghub.elsevier.com/retrieve/pii/S0378111915012433en
dc.rightsNOTICE: this is the author’s version of a work that was accepted for publication in Gene. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Gene, 28 October 2015. DOI: 10.1016/j.gene.2015.10.035en
dc.subjectMetagenomicsen
dc.subjectDatabaseen
dc.subjectBioinformaticsen
dc.subjectBiodiversityen
dc.subjectComparative metagenomicsen
dc.subjectMarine scienceen
dc.subjectMicrobeen
dc.subjectEnvironmenten
dc.titleDatabases of the marine metagenomicsen
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalGeneen
dc.eprint.versionPost-printen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorMineta, Katsuhikoen
kaust.authorGojobori, Takashien
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