#OptiVac - Designing String-of-beads with optimal spacers
Authors: Benjamin Schubert and Oliver Kohlbacher
Date: June 2015
Version: 1.0
License: This software is under a three-clause BSD license
The software is a novel approach to construct epitope-based string-of-beads vaccines in optimal order and with sequence-optimized spacers of flexible length such that the recovery of contained epitopes is maximized and immunogenicity of arising neo-epitopes is reduced.
Spacer Design uses the following software and libraries:
- Python 2.7 (https://www.python.org/)
- Fred2 (https://github.com/FRED-2/Fred2)
- Cplex >= 12.5 (www.ilog.com)
- LKH TSP-Approximation >= 2.0.7 (http://www.akira.ruc.dk/~keld/research/LKH/)
Please make sure you have installed said software/libraries and their dependencies.
First install all required software and libraries. CPLEX/LKH should be globally executable via command line.
usage: OptiVac.py [-h] -i INPUT -a ALLELES [-k MAX_LENGTH] [-al ALPHA]
[-be BETA] [-cp CLEAVAGE_PREDICTION]
[-ep EPITOPE_PREDICTION] [-thr THRESHOLD] -o OUTPUT
[-t THREADS]
The software is a novel approach to construct epitope-based string-of-beads vaccines in optimal order and with sequence-optimized spacers of flexible length such that the recovery of contained epitopes is maximized and immunogenicity of arising neo-epitopes is reduced.
Arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
File containing epitopes (one peptide per line)
-a ALLELES, --alleles ALLELES
Specifies file containing HLA alleles with
corresponding HLA probabilities (one HLA per line)
-k MAX_LENGTH, --max_length MAX_LENGTH
Specifies the max. length of the spacers (default 6)
-al ALPHA, --alpha ALPHA
Specifies the first-order preference of the user in
the model [0,1] (default 0.99)
-be BETA, --beta BETA
Specifies the second-order preference of the user in
the model [0,1] (default 0).
-cp CLEAVAGE_PREDICTION, --cleavage_prediction CLEAVAGE_PREDICTION
Specifies the used cleavage prediction method (default
PCM) [available: PCM, ProteaSMMConsecutive, ProteaSMMImmuno]
-ep EPITOPE_PREDICTION, --epitope_prediction EPITOPE_PREDICTION
Specifies the used epitope prediction method (default
Syfpeithi) [available: Syfpeithi, BIMAS, SMM, SMMPMBEC]
-thr THRESHOLD, --threshold THRESHOLD
Specifies epitope prediction threshold for SYFPEITHI
(default 20).
-o OUTPUT, --output OUTPUT
Specifies the output file.
-t THREADS, --threads THREADS
Specifies number of threads. If not specified all
available logical cpus are used.
python OptiVac.py -i example/epitope_list.csv -a example/allele_probabilities_europe.csv -o example/out.txt
Please cite:
Benjamin Schubert
schubert@informatik.uni-tuebingen.de
University of Tübingen, Applied Bioinformatics,
Center for Bioinformatics, Quantitative Biology Center,
and Dept. of Computer Science,
Sand 14, 72076 Tübingen, Germany