ojcharles / viral_antigen_map

Relating IEDB herpes antigenic sites to nucleotide position of reference strain using tblastn

viral_antigen_map

This is a repo that takes Immune Epitope Database and Analysis Resource "IEDB" data for a set of viruses, and maps it to their reference strain nucleotide position.

Requirements

the blast cli's in your path base R

Usage

go to https://www.iedb.org/ Download some data for your favourite virus (or anything I guess) , name it | species |.csv Pop the genome fasta of the reference genome in ./ref/| species |.fasta Run Rscript main.R | species |

a iedb database with reference start and reference end nucleotide positions will appear

todo optional

• make getting data automatic