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