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

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...

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Detalles Bibliográficos
Autores principales: Fowler, Douglas M., Araya, Carlos L., Gerard, Wayne, Fields, Stanley
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232369/
https://www.ncbi.nlm.nih.gov/pubmed/22006916
http://dx.doi.org/10.1093/bioinformatics/btr577
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author Fowler, Douglas M.
Araya, Carlos L.
Gerard, Wayne
Fields, Stanley
author_facet Fowler, Douglas M.
Araya, Carlos L.
Gerard, Wayne
Fields, Stanley
author_sort Fowler, Douglas M.
collection PubMed
description 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.
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spelling pubmed-32323692011-12-07 Enrich: software for analysis of protein function by enrichment and depletion of variants Fowler, Douglas M. Araya, Carlos L. Gerard, Wayne Fields, Stanley Bioinformatics Applications Note 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. Oxford University Press 2011-12-15 2011-10-17 /pmc/articles/PMC3232369/ /pubmed/22006916 http://dx.doi.org/10.1093/bioinformatics/btr577 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Note
Fowler, Douglas M.
Araya, Carlos L.
Gerard, Wayne
Fields, Stanley
Enrich: software for analysis of protein function by enrichment and depletion of variants
title Enrich: software for analysis of protein function by enrichment and depletion of variants
title_full Enrich: software for analysis of protein function by enrichment and depletion of variants
title_fullStr Enrich: software for analysis of protein function by enrichment and depletion of variants
title_full_unstemmed Enrich: software for analysis of protein function by enrichment and depletion of variants
title_short Enrich: software for analysis of protein function by enrichment and depletion of variants
title_sort enrich: software for analysis of protein function by enrichment and depletion of variants
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232369/
https://www.ncbi.nlm.nih.gov/pubmed/22006916
http://dx.doi.org/10.1093/bioinformatics/btr577
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