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



Last edited Oct 15, 2008 at 8:59 PM by CarlK, version 2

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