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A whole-genome bioinformatics approach to selection of antigens for systematic antibody generation.

Proteomics (2008-07-26)
Lisa Berglund, Erik Björling, Kalle Jonasson, Johan Rockberg, Linn Fagerberg, Cristina Al-Khalili Szigyarto, Asa Sivertsson, Mathias Uhlén
RÉSUMÉ

Here, we present an antigen selection strategy based on a whole-genome bioinformatics approach, which is facilitated by an interactive visualization tool displaying protein features from both public resources and in-house generated data. The web-based bioinformatics platform has been designed for selection of multiple, non-overlapping recombinant protein epitope signature tags by display of predicted information relevant for antigens, including domain- and epitope sized sequence similarities to other proteins, transmembrane regions and signal peptides. The visualization tool also displays shared and exclusive protein regions for genes with multiple splice variants. A genome-wide analysis demonstrates that antigens for approximately 80% of the human protein-coding genes can be selected with this strategy.