Mobile genetic elements (MGEs) are genetic entities that seek to replicate themselves and spread from cell to cell. Two of the most common forms of MGEs are viruses and plasmids. They can be found in virtually all of Earth's ecosystems.
called geNomad identifies and classifies MGEs based upon their gene content and their genetic sequences.
The software was created by researchers under the direction of Microbiome Data Science Group Lead Nikos Kyrpides at the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility at Lawrence Berkeley National Laboratory. geNomad is now accessible through the National Microbiome Data Collaborative's EDGE platform.
In order to gain more insights into Earth's ecosystems, researchers must examine the interactions that happen between tiny organisms located in soils and water.and evolution. This is because MGEs can affect a microbe's ability to cycle nutrients or produce new chemicals. They can also affect ecosystems by killing other cells.
Over time, MGEs can help microbes gain a competitive edge within an ecosystem. They influence the composition of the biogeochemical cycles around them. By understanding more about the genomics of MGEs and their evolution at thegeNomad is an annotation and classification framework that combines and builds on two standard techniques for identifying viruses and plasmids. Until now, most other tools have focused on identifying only specific plasmids or viruses.
geNomad employs two distinct approaches to identify both viruses and plasmids; one is marker gene-based, and the second is a neural network approach.
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