Journal ArticleDOI
Accurate and universal delineation of prokaryotic species
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TLDR
The specI (species identification tool) as mentioned in this paper ) is a method to group organisms into species clusters based on 40 universal, single-copy phylogenetic marker genes, applied to 3,496 prokaryotic genomes, specI identified 1,753 species clusters.Abstract:
The exponentially increasing number of sequenced genomes necessitates fast, accurate, universally applicable and automated approaches for the delineation of prokaryotic species. We developed specI (species identification tool; http://www.bork.embl.de/software/specI/), a method to group organisms into species clusters based on 40 universal, single-copy phylogenetic marker genes. Applied to 3,496 prokaryotic genomes, specI identified 1,753 species clusters. Of 314 discrepancies with a widely used taxonomic classification, >62% were resolved by literature support.read more
Citations
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Journal ArticleDOI
Metagenomic profiling of host-associated bacteria from 8 datasets of the red alga Porphyra purpurea with MetaPhlAn3
TL;DR: In this article, the bacterial-associated diversity of Porphyra purpurea in four different localities (Ireland, Italy United Kingdom and the USA) from analyzing eight publicly available metagenomic datasets was reported.
Book ChapterDOI
An Introduction to Whole-Metagenome Shotgun Sequencing Studies.
Tyler A. Joseph,Itsik Pe'er +1 more
TL;DR: In this paper, the authors provide an introduction to whole-metagenome shotgun sequencing, a ubiquitous approach for characterizing microbial communities, by reviewing three major research areas in metagenomics: assembly, community profiling, and functional profiling.
Posted ContentDOI
NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language
Luis Pedro Coelho,Renato J. Alves,Paulo P. Monteiro,Jaime Huerta-Cepas,Ana T. Freitas,Peer Bork +5 more
TL;DR: NG-meta-profiler, a fast profiler for metagenomes which performs sequence preprocessing, mapping to bundled databases, filtering of the mapping results, and profiling (taxonomic and functional) is developed.
Journal ArticleDOI
High-Quality Draft Genome Sequence of Arthrobacter sp. OY3WO11, a Strain That Inhibits the Growth of Phytophthora infestans.
TL;DR: The draft genome sequence of OY3WO11 may represent a novel species of Arthrobacter, which inhibits the growth of the potato pathogen Phytophthora infestans in in vivo growth challenge assays.
References
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Journal ArticleDOI
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Stephen F. Altschul,Thomas L. Madden,Alejandro A. Schäffer,Jinghui Zhang,Zheng Zhang,Webb Miller,David J. Lipman +6 more
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