title: Enrich: software for analysis of protein function by enrichment and depletion of variants.
abstract: CONCLUSIONS
  Measuring the consequences of mutation in proteins is critical to understanding their function. These measurements are essential in such applications as protein engineering, drug development, protein design and genome sequence analysis. Recently, high-throughput sequencing has been coupled to assays of protein activity, enabling the analysis of large numbers of mutations in parallel. We present Enrich, a tool for analyzing such deep mutational scanning data. Enrich identifies all unique variants (mutants) of a protein in high-throughput sequencing datasets and can correct for sequencing errors using overlapping paired-end reads. Enrich uses the frequency of each variant before and after selection to calculate an enrichment ratio, which is used to estimate fitness. Enrich provides an interactive interface to guide users. It generates user-accessible output for downstream analyses as well as several visualizations of the effects of mutation on function, thereby allowing the user to rapidly quantify and comprehend sequence-function relationships.
  
  
  METHODS
  Enrich is implemented in Python and is available under a FreeBSD license at http://depts.washington.edu/sfields/software/enrich/. Enrich includes detailed documentation as well as a small example dataset.
  
  
  BACKGROUND
  dfowler@uw.edu; fields@uw.edu
  
  
  BACKGROUND
  Supplementary data is available at Bioinformatics online.
authors: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. dfowler@uw.edu
authors: Douglas M
authors: DM
authors: Fowler
authors: Carlos L
authors: CL
authors: Araya
authors: Wayne
authors: W
authors: Gerard
authors: Stanley
authors: S
authors: Fields
mesh_terms: D019295:Computational Biology; D004252:DNA Mutational Analysis; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D009154:Mutation; D011506:Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D012984:Software
chemical_list: D011506:Proteins