PuLSE

PuLSE evaluates randomness and diversity in phage display libraries by analysing fastq sequence reads to quantify DNA base and translated peptide representation for library quality control.

Key Features:

• Randomness Assessment: Evaluates the randomness of DNA sequences within phage display libraries to detect deviations from expected incorporation rates of DNA bases.
• Sequence Analysis: Processes sequence reads in the fastq file format and generates tables profiling counts of unique DNA sequences, their positions, and translated peptide sequences.
• Expected Occurrence Calculation: Calculates normalized 'expected' occurrences from base-to-residue codon frequencies to estimate sequence representation across the library.
• Quantitative Quality Control: Provides quantitative quality-control metrics including sequence coverage at both the DNA base level and the translated protein residue level.

Scientific Applications:

• Antibody Development: Ensures library diversity to increase the likelihood of identifying high-affinity antibodies.
• Peptide Discovery: Assesses library representation to support exploration of novel peptides for therapeutic or industrial applications.
• Protein Engineering: Evaluates sequence diversity to facilitate identification and optimization of proteins with desired characteristics.

Methodology:

Analyzes sequence reads from phage display libraries (fastq), generates detailed tables of unique DNA sequences with positions and translated peptide sequences, and computes normalized 'expected' occurrences from codon frequencies to quantify library randomness and coverage.