Epitope Coverage Assessment Tool - Epicover
Purpose: Given a putative vaccine or antigen protein 'cocktail', or a set of such cocktails, and a test set of natural or background proteins, this tool will calculate the proportion of all epitope-length peptides in the test sequence set that are 'covered' (i.e., matched) by some peptide or peptides in each protein cocktail. Results are expressed as mean epitope-coverage over all test sequences.
Options include epitope length, the number of mismatches in each epitope to score (from zero to the maximum you set), and a rarity limit (epitope-length fragments occurring in fewer than this minimum number of sequences will be ignored).
Advanced options involve separately reporting results for subsets of the test protein set. You can provide a file of grouped sequence names [example of format] or you may request the program to group the sequences by looking at their names. These options can be combined.
Usage: Paste your amino acid sequences in the boxes below, or use the browse button to select files on your computer that contain sequences to upload. Inputs may be combined. Sequences with toggles may be used, and most common sequence formats are accepted.
Related Programs:
Contributors:
- Jim Thurmond - web implementation and perl programming (at lanl.gov, email address 'thurmond'),
- Will Fischer - perl programming (at lanl.gov, email address 'wfischer'),
Useful Links: Polyvalent vaccine design article | PubMed version