Computational protocol: Computer-Aided Design of an Epitope-Based Vaccine against Epstein-Barr Virus

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Protocol publication

[…] We used CD-HIT [] with default settings to generate clusters from 13,899 EBV protein sequences that included 89 translated coding DNA sequences (CDS) from a reference genome virus (accession: NC_007605). The protein sequences were downloaded following the links in the NCBI taxonomy database (TAX ID: 10376) []. We processed CD-HIT clusters with reference EBV proteins, removed identical sequences, and subsequently generated multiple sequence alignments (MSA) using MUSCLE []. As a result, we obtained 85 referenced MSA of EBV proteins that were used for further analysis. Software for clustering the sequences will be provided by the corresponding author upon written request. […]

Pipeline specifications

Software tools CD-HIT, MUSCLE
Databases NCBI Taxonomy Database
Application Nucleotide sequence alignment
Organisms Human gammaherpesvirus 4, Homo sapiens, Human poliovirus 1 Mahoney