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Updated: Mar 23, 2026

Directed Evolution Method in Saccharomyces cerevisiae: Mutant Library Creation and Screening

Directed Evolution Method in Saccharomyces cerevisiae: Mutant Library Creation and Screening

Published on: April 1, 2016

ScaffoldSeq: Software for characterization of directed evolution populations.

Daniel R Woldring¹, Patrick V Holec¹, Benjamin J Hackel¹

¹Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, 55455.

|March 29, 2016

Summary

This summary is machine-generated.

ScaffoldSeq software analyzes DNA sequences from protein engineering experiments. It characterizes amino acid frequencies and interactions, overcoming challenges posed by variable sequence lengths and experimental biases.

Keywords:

bioinformatics epistasis family clustering high-throughput sequence analysis software

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Published on: June 28, 2018

Area of Science:

Protein engineering and bioinformatics
Computational biology and drug discovery

Background:

High-throughput sequencing generates large DNA populations for protein analysis.
Analyzing protein diversity is crucial for applications like enzyme maturation and antibody screening.
Sequence and length variability in diversified protein regions complicate traditional alignment methods.

Purpose of the Study:

To introduce ScaffoldSeq, a novel software for analyzing DNA sequence populations in protein engineering.
To address challenges in sequence alignment due to length variability in diversified protein regions.
To provide tools for quantifying and correcting experimental biases in sequence frequency data.

Main Methods:

ScaffoldSeq algorithm leverages conserved framework sequences to rapidly identify diverse protein regions.
Utilizes tools to quantify and remove background sequences, cluster protein families, and mitigate dominant clone effects.
Generates site-specific and pairwise amino acid frequency summaries for diversity evaluation.

Main Results:

ScaffoldSeq effectively handles length variability in diversified protein regions, facilitating alignment.
The software quantifies and corrects unintended biases in sequence frequency data from experimental workflows.
Enables detailed analysis of site-specific diversity and identification of epistatic pairwise interactions.

Conclusions:

ScaffoldSeq provides a robust solution for characterizing protein sequence diversity in directed evolution.
The software aids in understanding protein function and optimizing engineering strategies.
ScaffoldSeq is freely available, promoting advancements in protein engineering research.