Deep Mutational Scanning: Calculating Enrichment Scores for Protein Variants from DNA Sequencing Output Files

Lea M Starita; Stanley Fields

doi:10.1101/pdb.prot085233

Deep Mutational Scanning: Calculating Enrichment Scores for Protein Variants from DNA Sequencing Output Files

Cold Spring Harb Protoc. 2015 Aug 3;2015(8):781-3. doi: 10.1101/pdb.prot085233.

Authors

Lea M Starita¹, Stanley Fields²

Affiliations

¹ Department of Genome Sciences, University of Washington, Seattle, Washington 98195;
² Department of Genome Sciences, University of Washington, Seattle, Washington 98195; Department of Medicine, University of Washington, Seattle, Washington 98195; Howard Hughes Medical Institute, Seattle, Washington 98195.

PMID: 26240406
DOI: 10.1101/pdb.prot085233

Abstract

During a deep mutational scanning experiment, a collection of variants of a given protein is subjected to high-throughput sequencing before and after selection. The variants that perform well during selection will increase in abundance, whereas those that perform poorly will decrease. Generating a sequence-function map of a protein from a deep mutational scan requires the calculation and comparison of the enrichment scores for each protein variant, based on the results of high-throughput DNA sequencing output files. Here we describe the use of the software program Enrich, which was written specifically for the data analysis phase of a deep mutational scanning experiment.

MeSH terms

Computational Biology / methods*
DNA Mutational Analysis / methods*
Genetic Testing / methods*
High-Throughput Nucleotide Sequencing / methods
High-Throughput Screening Assays / methods*
Molecular Biology / methods*
Software*