Efficient mapping of short peptides on whole proteome database for biomarker discovery
Résumé
In vivo phage display can be used to simultaneously screen peptide repertoires for peptides presenting specificity for certain interaction and recognition sites, and thus enable biomarker identification. In this work we assume the hypothesis that certain small peptides mimic physiological interactions of proteins that contain a sub-sequence similar to these peptides. A possible solution then involves mapping of the peptide repertoire against the proteome of interest, which is computationally challenging. We formulate this problem as simultaneous matching of multiple patterns against multiple strings and propose an algorithmically efficient solution. It is currently accessible at http://services.cbib.u-bordeaux2.fr/spack/pepteam.php.
Origine : Fichiers produits par l'(les) auteur(s)
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