CreateEpitome.exe
Usage
HlaCompletion {-stopLength 10000} inputFile outputFile
- where the optional -stopLength tells the program to stop the vaccine at the given amino acid length
Input Format
The input is a tab-delimited file with two columns: Patch & Weight
- A patch is a peptide, for example, NKIVRMYSP
- A weight is a number, for example, 167
Example:
Patch Weight
NKIVRMYSP 167
LNKIVRMYS 167
PQDLNTMLN 166
QDLNTMLNT 166
GATPQDLNT 166
EGATPQDLN 166
ATPQDLNTM 165
TPQDLNTML 165
Output Format Example
Method AminoAcidLength numComponents coverage Vaccine
Greedy 9 1 0.125753012048193 LNKIVRMYS
Greedy 10 1 0.251506024096386 LNKIVRMYSP
Greedy 17 1 0.376506024096386 PQDLNTMLNKIVRMYSP
Greedy 18 1 0.500753012048193 TPQDLNTMLNKIVRMYSP
Greedy 19 1 0.625 ATPQDLNTMLNKIVRMYSP
Greedy 20 1 0.75 GATPQDLNTMLNKIVRMYSP
Greedy 21 1 0.875 EGATPQDLNTMLNKIVRMYSP
Greedy 30 2 1 EGATPQDLNTMLNKIVRMYSP,QDLNTMLNT