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
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BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
Felipe A. Simão,Robert M. Waterhouse,Panagiotis Ioannidis,Evgenia V. Kriventseva,Evgeny M. Zdobnov +4 more
TL;DR: Zdobnov et al. as discussed by the authors proposed a measure for quantitative assessment of genome assembly and annotation completeness based on evolutionarily informed expectations of gene content, and implemented the assessment procedure in open-source software, with sets of Benchmarking Universal Single-Copy Orthologs.
Journal ArticleDOI
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
TL;DR: An objective measure of genome quality is proposed that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities and is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches.
BUSCO: Assessing Genome Assembly and Annotation Completeness with Single-Copy Orthologs
TL;DR: This work proposes a measure for quantitative assessment of genome assembly and annotation completeness based on evolutionarily informed expectations of gene content, implemented in open-source software, with sets of Benchmarking Universal Single-Copy Orthologs, named BUSCO.
Journal ArticleDOI
NCBI prokaryotic genome annotation pipeline
Tatiana Tatusova,Michael DiCuccio,Azat Badretdin,Vyacheslav Chetvernin,Eric P. Nawrocki,Leonid Zaslavsky,Alexandre Lomsadze,Kim D. Pruitt,Mark Borodovsky,James Ostell +9 more
TL;DR: The new NCBI's Prokaryotic Genome Annotation Pipeline (PGAP) relies less on sequence similarity when confident comparative data are available, while it relies more on statistical predictions in the absence of external evidence.
Journal ArticleDOI
Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes
TL;DR: The overall distribution of ANI values generated by pairwise comparison of 6787 genomes of prokaryotes belonging to 22 phyla was investigated, finding an apparent distinction in the overall ANI distribution between intra- and interspecies relationships at around 95-96% ANI.
References
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Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypes
TL;DR: Direct evidence supporting the coexistence and distribution of multiple ecotypes permits the survival of the population as a whole over a broader range of environmental conditions than would be possible for a homogeneous population is reported.
Journal ArticleDOI
Comparison of Methods Based on Different Molecular Epidemiological Markers for Typing of Mycobacterium tuberculosis Complex Strains: Interlaboratory Study of Discriminatory Power and Reproducibility
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eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges
Sean Powell,Damian Szklarczyk,Kalliopi Trachana,Alexander Roth,Michael Kuhn,Jean Muller,Roland Arnold,Thomas Rattei,Ivica Letunic,Tobias Doerks,Lars Juhl Jensen,Christian von Mering,Peer Bork +12 more
TL;DR: The third version of the eggNOG database contains non-supervised orthologous groups constructed from 1133 organisms, doubling the number of genes with orthology assignment compared to eggNog v2 and the newly designed web page is considerably faster with more functionality.
Journal ArticleDOI
eggNOG: automated construction and annotation of orthologous groups of genes
Lars Juhl Jensen,Philippe Julien,Michael Kuhn,Christian von Mering,Jean Muller,Tobias Doerks,Peer Bork +6 more
TL;DR: The eggNOG database is presented (‘evolutionary genealogy of genes: Non-supervised Orthologous Groups’), which contains orthologous groups constructed from Smith–Waterman alignments through identification of reciprocal best matches and triangular linkage clustering.
Journal ArticleDOI
Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2
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