Epitope Prediction Workflow

Download Dengue Sequence

• Step-1: Go To - https://www.viprbrc.org/brc/viprDetails.spgncbiProteinId=VIPR_ALG4_570348514_13404_16201&decorator=corona
• Step-2: Click Search Data
• Step-3: Virus Family > Flaviviridae
• Step-4: Featured Viruses > Dengue Virus
• Step-5: Search Data > Search Sequences > Genes & Proteins
• Step-6: GENE SYMBOL > Select E(Envelope Protein) > Click Search
• Step-7: Click Checkbox > End of the Page > Download > Protein FASTA

Initial Steps

• Open File with MS Word
• Check Length

Epitope Prediction: MHC-I Binding

• Step-1: Go to https://www.iedb.org/
• Step-2: Epitope Analysis Resource > T Cell Epitope Prediction > MCH-I Binding
• Step-3: Enter protein sequence(s) in FASTA format or as whitespace-separated sequences or Or select file containing sequence(s)
• Step-4: Show only frequently occuring alleles: Select MHC allele(s) > Allele > HLA-A*01:01 > Length > 9
• Step-5: Repeat: Show only frequently occuring alleles: Select MHC allele(s) > Allele > HLA-A*01:01 > Length > 9
• Step-6: Submit

Epitope Prediction: MHC-II Binding

• Step-1: Go to https://www.iedb.org/
• Step-2: Epitope Analysis Resource > T Cell Epitope Prediction > MCH-II Binding
• Step-3: Enter protein sequence(s) in FASTA format or as whitespace-separated sequences or Or select file containing sequence(s)
• Step-4: Show only frequently occuring alleles: Select MHC allele(s) > Allele > DRB1*01:01 > Length > 15
• Step-5: Repeat: Show only frequently occuring alleles: Select MHC allele(s) > Allele > DRB1*01:03 > Length > 15
• Step-6: Submit

Team

• Shaheen Alam[Team Lead, Genomics], shaheen@hdrobd.org
• Mehedi Hasan, mehedi@hdrobd.org
• Jubayer Hossain, jubayer@hdrobd.org
• Rubaiya Gulshan Meem, rubaiya@hdrobd.org
• Sumaiya Akter Mukta, sumaiya@hdrobd.org
• Aminul Islam, aminul@hdrobd.org
• Sharif Miah, sharif@hdrobd.org