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A unified compendium of prokaryotic and viral genomes from over 300 anaerobic digestion microbiomes
BackgroundThe anaerobic digestion process degrades organic matter into simpler compounds and occurs in strictly anaerobic and microaerophilic...
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A global survey of prokaryotic genomes reveals the eco-evolutionary pressures driving horizontal gene transfer
Horizontal gene transfer, the exchange of genetic material through means other than reproduction, is a fundamental force in prokaryotic genome...
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Translation Comes First: Ancient and Convergent Selection of Codon Usage Bias Across Prokaryotic Genomes
Codon usage is the outcome of different evolutionary processes and can inform us about the conditions in which organisms live and evolve. Here, we...
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VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes
BackgroundWith the advent of metagenomics, the importance of microorganisms and how their interactions are relevant to ecosystem resilience,...
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A combined de novo assembly approach increases the quality of prokaryotic draft genomes
Next-generation sequencing methods provide comprehensive data for the analysis of structural and functional analysis of the genome. The draft genomes...
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PRFect: a tool to predict programmed ribosomal frameshifts in prokaryotic and viral genomes
BackgroundOne of the stranger phenomena that can occur during gene translation is where, as a ribosome reads along the mRNA, various cellular and...
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GUNC: detection of chimerism and contamination in prokaryotic genomes
Genomes are critical units in microbiology, yet ascertaining quality in prokaryotic genome assemblies remains a formidable challenge. We present GUNC...
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Chemotaxonomy and Genomes
Chemotaxonomy or chemical taxonomy is the identification and classification of an organism based on the differences or similarities of the chemical...
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A multi-kingdom collection of 33,804 reference genomes for the human vaginal microbiome
The human vagina harbours diverse microorganisms—bacteria, viruses and fungi—with profound implications for women’s health. Genome-level analysis of...
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Nitrogen and sulfur metabolisms encoded in prokaryotic communities associated with sea ice algae
Sea ice habitats harbour seasonally abundant microalgal communities, which can be highly productive in the spring when the availability of light...
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Annotation and Comparative Genomics of Prokaryotic Transposable Elements
The data generated in nearly 30 years of bacterial genome sequencing has revealed the abundance of transposable elements (TE) and their importance in...
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Comparative Analyses of Bacteriophage Genomes
Bacterial viruses (bacteriophages or phages) are the most abundant and diverse biological entities on Earth. There is a renewed worldwide interest in...
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Stratification of Prokaryotic Communities in the White Sea Bottom Sediments
Abstract —Investigation of prokaryotic communities from different horizons of the bottom sediments in the Kandalaksha Gulf, White Sea revealed two...
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Prokaryotic Argonaute Proteins as a Tool for Biotechnology
AbstractProgrammable nucleases are the most important tool for manipulating the genes and genomes of both prokaryotes and eukaryotes. Since the end...
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Pseudogenes act as a neutral reference for detecting selection in prokaryotic pangenomes
A long-standing question is to what degree genetic drift and selection drive the divergence in rare accessory gene content between closely related...
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The association of prokaryotic antiviral systems and symbiotic phage communities in drinking water microbiomes
Prokaryotic antiviral systems are important mediators for prokaryote-phage interactions, which have significant implications for the survival of...
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Contrasting drivers of abundant phage and prokaryotic communities revealed in diverse coastal ecosystems
Phages (viruses of bacteria and archaea) are a ubiquitous top-down control on microbial communities by selectively infecting and killing cells. As...
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Prokaryotic Genome Annotation
In the last decade, the high-throughput and relatively low cost of short-read sequencing technologies have revolutionized prokaryotic genomics. This...
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Large language models improve annotation of prokaryotic viral proteins
Viral genomes are poorly annotated in metagenomic samples, representing an obstacle to understanding viral diversity and function. Current annotation...
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Structural features of fungal genomes
Eighteen fungal genomes have been sequenced to date from a variety of taxonomic groups, with fifteen Ascomycota, two Basidomycota and one...