Reference Gene Modules - CDCgov/HantaNet GitHub Wiki

Description

  • Three reference gene modules for the hantavirus segmented genome: Small (nucleocapsid), Medium (glycoprotein), Large (RNA-dependent RNA polymerase)

Reference-Gene-Modules

  • Curated metadata and fasta files of aligned sequences (sourced from GenBank/ViPR)
  • Metadata files include strain classification of hantaviruses (SNV, NYV, SEOV, etc)
  • Fasta files include clean and complete gene coding sequence (CDS); stop codon removed
  • NCBI Accession ID is used to match the metadata with the sequence data
  • The same Virus ID is assigned to Small, Medium and Large gene sequences belonging to the same virus
  • Reference collection dates: 1982 – 2017

Available view options

  • Default view is 2D Network: Uses TN93 substitution model to compute genetic distances, then builds a molecular network
  • Default genetic distance: 0.15 - 0.20 (hantavirus strain-specific clusters)
  • Build and customize dashboards with additional view options, including Map and Phylogenetic Tree views

2D Network

2D-Network

Phylogenetic Tree

phylo-tree

Phylogenetic Tree Dashboard

Importing-Trees

Map Dashboard

Spatial-Temporal

Transmission Networks

Overlay-epi-genetic-data