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Deep sequencing is a rapid DNA sequencing technique that is useful for characterizing virome richness, stability, gene function and the association with disease phenotypes. [ 1 ] [ 3 ] This technology creates large amounts of sequence information and is capable of detecting rare components of a microbial community.
Virome refers to the assemblage of viruses [1] [2] that is often investigated and described by metagenomic sequencing of viral nucleic acids [3] that are found associated with a particular ecosystem, organism or holobiont. The word is frequently used to describe environmental viral shotgun metagenomes.
The Global Virome Project (GVP) is an American-led international collaborative research initiative based at the One Health Institute at the University of California, Davis. [ 1 ] [ 2 ] The project was co-launched by EcoHealth Alliance president Peter Daszak , Nathan Wolfe and Edward Rubin of Metabiota , and former Chinese Center for Disease ...
One such surveillance program is the Global Virome Project (GVP) an international collaborative research initiative based at the One Health Institute at the University of California, Davis. [ 29 ] [ 30 ] The GVP aims to boost infectious disease surveillance around the globe by using low cost sequencing methods in high risk countries to prevent ...
The sequence-driven approach to screening is limited by the breadth and accuracy of gene functions present in public sequence databases. In practice, experiments make use of a combination of both functional and sequence-based approaches based upon the function of interest, the complexity of the sample to be screened, and other factors.
Serratus is a large scale viroinformatics platform for uncovering the total genetic diversity of Earth's virome.Originating with the goal of uncovering novel coronaviruses [1] that may have been incidentally sequenced by other researchers, the project expanded to encompass all RNA viruses, those which encode a viral RNA-dependent RNA polymerase (RdRp).
ProViDE adopts the reverse orthology based approach similar to SOrt-ITEMS for the taxonomic classification of metagenomic sequences obtained from virome datasets. It a customized set of BLAST parameter thresholds, specifically suited for viral metagenomic sequences.
Sequences that are believed to be derived from unknown microbes are referred to as the microbial dark matter, [18] the dark virome, [19] or dark matter fungi. [20] Such sequences are not rare. It has been estimated that in material from humans, between 40 and 90% of viral sequences are from dark matter.
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