Display Settings:

Format

Send to:

Choose Destination
See comment in PubMed Commons below
Bioinformatics. 2011 Dec 15;27(24):3430-1. doi: 10.1093/bioinformatics/btr577. Epub 2011 Oct 17.

Enrich: software for analysis of protein function by enrichment and depletion of variants.

Author information

  • 1Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. dfowler@uw.edu

Abstract

SUMMARY:

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.

AVAILABILITY AND IMPLEMENTATION:

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.

CONTACT:

dfowler@uw.edu; fields@uw.edu

SUPPLEMENTARY INFORMATION:

Supplementary data is available at Bioinformatics online.

PMID:
22006916
[PubMed - indexed for MEDLINE]
PMCID:
PMC3232369
Free PMC Article

Images from this publication.See all images (1)Free text

Fig. 1.
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Icon for HighWire Icon for PubMed Central
    Loading ...
    Write to the Help Desk