Application of Deep Sequencing in Phage Display

Abstract

This chapter describes the workflow to implement deep sequencing into standard phage display experiments on protein libraries. By harvesting the power of high throughput of these techniques, it allows for comprehensive analysis of the naïve library and library evolution in response to selection by ligand binding. The mutagenized target region of the protein variants encoded by the phage pool is analyzed by Illumina paired-end sequencing. Sequence data are processed to extract selection-enriched amino acid motifs. In addition, a complementary long-read sequencing approach is proposed enabling the monitoring of display vector stability.

Keywords: Enrichment detection; Illumina sequencing; Indel detection; Molecular evolution; Next-generation sequencing; Oxford Nanopore sequencing; Phage display.