An efficient algorithm for large-scale detection of protein families

Enright, Anton J.; Dongen, Stijn van; Ouzounis, Christos A.

doi:10.1093/nar/30.7.1575

Cited by 3,237 publications

(3,109 citation statements)

References 49 publications

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“…log-transformed e-value, and MCL inflation of 2 63 ). vContact (https://bitbucket.org/MAVERICLab/ vcontact) was then used to calculate a similarity score between every pair of genome and/or contigs based on the number shared of PCs between the two sequences (as in 8,9 ), and then compute a MCL clustering of the genomes/contigs based on these similarity scores (thresholds of 1 on similarity score, MCL inflation of 2).…”

Section: Dataset Of Publicly Available Viral Genomes and Genome Fragmmentioning

confidence: 99%

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

Roux

Brum

Dutilh

et al. 2016

Nature

641

885

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Tara Oceans CoordinatorsInternational audienceOcean microbes drive biogeochemical cycling on a global scale. However, this cycling is constrained by viruses that affect community composition, metabolic activity, and evolutionary trajectories. Owing to challenges with the sampling and cultivation of viruses, genome-level viral diversity remains poorly described and grossly understudied, with less than 1% of observed surface-ocean viruses known. Here we assemble complete genomes and large genomic fragments from both surface- and deep-ocean viruses sampled during the Tara Oceans and Malaspina research expeditions, and analyse the resulting ‘global ocean virome’ dataset to present a global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts. A total of 15,222 epipelagic and mesopelagic viral populations were identified, comprising 867 viral clusters (defined as approximately genus-level groups. This roughly triples the number of known ocean viral populations and doubles the number of candidate bacterial and archaeal virus genera, providing a near-complete sampling of epipelagic communities at both the population and viral-cluster level. We found that 38 of the 867 viral clusters were locally or globally abundant, together accounting for nearly half of the viral populations in any global ocean virome sample. While two-thirds of these clusters represent newly described viruses lacking any cultivated representative, most could be computationally linked to dominant, ecologically relevant microbial hosts. Moreover, we identified 243 viral-encoded auxiliary metabolic genes, of which only 95 were previously known. Deeper analyses of four of these auxiliary metabolic genes (dsrC, soxYZ, P-II (also known as glnB) and amoC) revealed that abundant viruses may directly manipulate sulfur and nitrogen cycling throughout the epipelagic ocean. This viral catalog and functional analyses provide a necessary foundation for the meaningful integration of viruses into ecosystem models where they act as key players in nutrient cycling and trophic networks

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Section: Dataset Of Publicly Available Viral Genomes and Genome Fragmmentioning

confidence: 99%

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

Roux

Brum

Dutilh

et al. 2016

Nature

641

885

View full text Add to dashboard Cite

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“…These large proteins were further analyzed as potential class 2 Cas effectors. The potential effectors were clustered to protein families based on sequence similarities using MCL 46 . These protein families were expanded by building HMMs representing each of these families, and using them to search the metagenomic datasets for similar Cas proteins.…”

Section: Crispr-cas Computation Analysesmentioning

confidence: 99%

New CRISPR–Cas systems from uncultivated microbes

Burstein

Harrington

Strutt

et al. 2016

Nature

478

369

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CRISPR-Cas systems provide microbes with adaptive immunity by employing short sequences, termed spacers, that guide Cas proteins to cleave foreign DNA 1,2 . Class 2 CRISPR-Cas systems are streamlined versions in which a single Cas protein bound to RNA recognizes and cleaves targeted sequences 3,4 . The programmable nature of these minimal systems has enabled their repurposing as a versatile technology that is broadly revolutionizing biological and clinical research 5 . However, current CRISPR-Cas technologies are based solely on systems from isolated bacteria, leaving untapped the vast majority of enzymes from organisms that have not been cultured. Metagenomics, the sequencing of DNA extracted from natural microbial communities, provides access to the genetic material of a huge array of uncultivated organisms 6,7 . Here, using genome-resolved metagenomics, we identified novel CRISPR-Cas systems, including the first reported Cas9 in the archaeal domain of life. This divergent Cas9 protein was found in littlestudied nanoarchaea as part of an active CRISPR-Cas system. In bacteria, we discovered two

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“…It specifically searches for clusters with a strongly interconnected neighborhood, which is often the case in large scale biological interaction networks. MGclus was compared to a selection of widely used clustering methods including MCL, 20 CFinder, 18 FastCommunity, 19 MCode, 7 MINE, 21 NEMO, 5 SPICi, 22 and Cohtop. 23 Three different benchmarks were conducted.…”

Section: Resultsmentioning

confidence: 99%