PuLSE: Quality control and quantification of peptide sequences explored by phage display libraries

Area of Science:

• Molecular Biology
• Bioinformatics
• Drug Discovery

Background:

• Phage display library design assumes equal DNA base incorporation rates.
• Increasing library complexity reduces unique sequence copy numbers, necessitating true randomness.
• Sparse exploration of library space highlights the critical need for sequence randomness.

Purpose of the Study:

• To introduce PuLSE (Phage Library Sequence Evaluation), a novel computational tool.
• To assess the randomness and diversity of phage display libraries.
• To provide quantitative quality control for phage libraries at DNA and protein levels.

Main Methods:

• PuLSE analyzes sequence reads in fastq file format.
• It generates tables profiling unique DNA sequences and their positions.
• The tool also profiles translated peptide sequences and normalized codon frequencies.

Main Results:

• PuLSE provides quantitative quality control for phage libraries.
• It assesses sequence coverage at both DNA base and translated protein residue levels.
• The program identifies deviations from expected base and residue frequencies.

Conclusions:

• PuLSE addresses a gap in existing toolsets for phage library assessment.
• The software enables efficient and accurate evaluation of library diversity.
• PuLSE is available as open-source C++ code and precompiled binaries for broad accessibility.