Framework for determining optimal string-of-beads vaccines with spacer sequences of flexible length
Python
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
example
.gitignore
LICENSE
OptiVac.py
README.md

README.md

#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

Introduction:

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.

Requirement:

Spacer Design uses the following software and libraries:

  1. Python 2.7 (https://www.python.org/)
  2. Fred2 (https://github.com/FRED-2/Fred2)
  3. Cplex >= 12.5 (www.ilog.com)
  4. 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.

Installation:

First install all required software and libraries. CPLEX/LKH should be globally executable via command line.

Usage:

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.

Example

python OptiVac.py -i example/epitope_list.csv -a example/allele_probabilities_europe.csv -o example/out.txt

Citation

Please cite:

Schubert, B., & Kohlbacher, O. (2016). Designing string-of-beads vaccines with optimal spacers. Genome medicine, 8(1), 1.

Contacts:

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