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Vollständige Shotgun-DNA-Metagenomik

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Einführung in die Bioinformatik in der Mikrobiologie

Zusammenfassung

Die vollständige DNA-Metagenomik ist die Sequenzierung aller DNA aus einer Probe, gefolgt von Zusammenfügen und Annotation sowie Zuordnung von Sequenzinformationen zu Organismen und Funktionen. Das Assembly von DNA-Sequenz-Reads versucht, Genomfragmente zu Genomentwürfen zusammenzufügen. Die Bioinformatik-Pipelines mothur und QIIME, die in Kap. 8 für die 16S-rRNA-Amplicon-Sequenzanalyse vorgestellt wurden, können auch für die vollständige DNA-Metagenomik verwendet werden. Der Schwerpunkt in diesem Kapitel liegt auf MG-RAST, das sowohl die Informationen aus vorhergesagten Proteinen in Metagenomik-Daten für die weitere Vorhersage von Funktionen oder taxonomischen Beziehungen verarbeiten kann, als auch die 16S-rRNA-Gen-Sequenzinformationen extrahieren und detailliertere taxonomische Informationen aus den spezialisierten Datenbanken SILVA, Greengenes und RDP bereitstellen kann, die in Kap. 8 vorgestellt wurden. Die schwerwiegendste Einschränkung der vollständigen DNA-Metagenomik sind wahrscheinlich die Datenbanken, die hauptsächlich auf kultivierten Mikroorganismen basieren.

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Correspondence to Henrik Christensen .

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Christensen, H., Olsen, J.E. (2023). Vollständige Shotgun-DNA-Metagenomik. In: Christensen, H. (eds) Einführung in die Bioinformatik in der Mikrobiologie. Springer Vieweg, Cham. https://doi.org/10.1007/978-3-031-31212-0_9

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