Mosaic Vaccine Designer
Purpose: The Mosaic Vaccine Designer will generate candidate vaccine protein cocktails that optimize the coverage, by a small set of mosaic proteins that could be included in a vaccine cocktail, of potential T-cell epitopes in a large diverse set of proteins. The resulting 'mosaic' proteins in the proposed vaccine cocktail resemble real proteins from the input set of natural viral proteins (the 'training set'), but are assembled from fragments of the natural proteins using a genetic algorithm (a computational optimization method). This method was first applied to HIV, but is readily generalized and could be applied to other variable pathogens.
Functions:
- 'Create mosaic sequence cocktail' runs the genetic algorithm to generate a cocktail of synthetic sequences with near-optimal coverage
- 'Pick the best natural sequences' selects unmodified natural sequences from the training set in order of coverage
- 'See the coverage distribution of natural sequences' shows the coverages of a randomly selected set of natural sequence cocktails
Usage: Paste your protein sequences in the box below, or upload a file containing sequences. Most common sequence formats are accepted. Input sequences do not need to be aligned, and the results are alignment independent. As soon as your job is completed, a link to your results will be sent to your email address which you provided. To manage more detailed parameters, go to the Advanced Input. (Your job may take several hours or even days, according to your input.)
Download stand-alone Mosaic Vaccine Designer:
Related Programs:
Contributors:
- Hyejin Yoon - web implementation and perl programming (at lanl.gov, email address 'hyoon'),
- Will Fischer - perl programming (at lanl.gov, email address 'wfischer'),
- Simon Perkins - original algorithm and C programming (at ultraspectral.com, email address 'simon.perkins')
Useful Links: Polyvalent vaccine design article | PubMed version