Reference Gene Modules

Description

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

• 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

Phylogenetic Tree

Phylogenetic Tree Dashboard

Map Dashboard

Transmission Networks