Workflow from Scientific Research

Provirus identification starts by annotating the genes within a sequence with geNomad markers, which store information of how specific they are to hosts or viruses. These specificity values are then fed to a CRF model, which will score each gene using information from the markers in its surroundings. A score cutoff is used to demarcate viral islands, and islands that are close together are merged. Islands with few viral markers are discarded, and the boundaries of the remaining islands are extended up until nearby tRNAs or integrases.

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