insilico-vaccine-design-code

In silico Vaccine Design In-silico vaccine design takes advantage of the rapidly accumulating omics data: genomics and proteomic data is of particular interest in vaccine design. The continued development of bioinformatics tools has further driven the in-silico vaccine design process. Machine learning algorithms have increased the predictive ability to detect both B and T cell epitopes for creating vaccine constructs. Vaccine design relies on the ability to distinguish patterns on antigenic peptides that can potentially stimulate an immune response with ones that don’t. (Rötzschke et al., 1991) suggested that the predicted patterns could be used to find peptides that would bind to MHC, engage T cell receptors and stimulate T cell response, peptides that can elicit this response are T-cell epitopes. Bioinformatics tools have accelerated the prediction of these motifs and at the same time accelerated development of epitope-based vaccines. B cell epitopes have the ability to bind to immunoglobulins or antibodies and are of two type’s linear and conformational also known as continuous and discontinuous epitopes. A combination of B and T cell epitopes is often used to create chimeric peptides than can be used as vaccines. Predicted T-cell epitopes are usually at an optimal length of 9-10 mers while B-cell epitopes having varying lengths but usually the best being 15-22 amino acids in length.

The python code(generate_epitope_combinations.py) for the generation of multi-epitope vaccine constructs,this code is essential for the generation of vaccine constructs, the user has latitude to select the adjuvant and linkers for the B and T cell epitopes(edit the script to appropriate adjuvant and linkers) eg. tcell_linker='AAY', bcell_linker='GPGPG'.

usage:

python generate_epitope_combinations.py [-h] [-t TCELL] [-b BCELL] [-r RANDOMSIZE] [-tcl TCLINKER] [-bcl BCLINKER]

optional arguments:

-h, --help show this help message and exit

-r RANDOMSIZE, --randomsize RANDOMSIZE (number of randomized epitopes)

-tcl TCLINKER, --tclinker TCLINKER (T-cell epitopes linker)

-bcl BCLINKER, --bclinker BCLINKER (B-cell epitopes linker)

required arguments:

-t TCELL, --tcell TCELL (T-cell epitope file path)

-b BCELL, --bcell BCELL (B-cell epitope file path)

provide B & T cell epitopes in csv format as follows:

pos,epitope

1. 255 SEEKDTNSEEDPEAEEDPD
2. 295 IIPSPKPLTPEQQQERELKL
3. 272 SSSNGSSSSNSTSSSSSSTT
4. 251 ITKAIKKPNSGSTTSSSSNT
5. 24 NCKCHNNNSNSSSNNDTLGG
6. 438 VNSVSTVSPVNPVNPVNPVV
7. 490 AVNTSNPSNPVNTVNQVVNE