Computational protocol: Antibodies to the Glycoprotein GP2 Subunit Cross-React between Old and New World Arenaviruses

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Protocol publication

[…] Amino acid sequences from the indicated virus glycoproteins (or whole-genome sequences) were downloaded from GenBank with a preference for whole-genome sequences acquired from the field in a similar manner. These were then standardized by removal of all primer sequences and then (if applicable) translated using ExPASy (Swiss Institute of Bioinformatics), and amino acid sequences were extracted and labeled with short names as indicated below. A multiple sequence alignment (MSA) was generated using Clustal Omega, and the alignment file was analyzed using Jalview. Percent identity per position was then determined in Jalview as the percentage of utilized viral sequences that share the Lassa virus amino acid at each position. These percent identity values were then translated to heat map colors (blue is 100% shared; red is 0% shared) and visualized in Microsoft Excel. The map was then labeled and standardized so that each pixel corresponds to one amino acid in Adobe Illustrator CS6. The phylogenetic tree of the different GPCs was built using the neighbor-joining method based on amino acid sequences in Clustal Omega. The tree was then visualized and labeled in Figtree v1.4.1.3. […]

Pipeline specifications

Software tools Clustal Omega, Jalview, Adobe Illustrator, FigTree
Databases ExPASy
Applications Miscellaneous, Phylogenetics
Organisms Homo sapiens, Viruses, Lassa mammarenavirus, Machupo mammarenavirus, Mus musculus, Human poliovirus 1 Mahoney
Diseases Hemorrhagic Fever, American, Vesicular Stomatitis