{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,11]],"date-time":"2026-06-11T01:13:19Z","timestamp":1781140399800,"version":"3.54.1"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1812,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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\u2013function relationships.<\/jats:p>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Contact: \u00a0dfowler@uw.edu; fields@uw.edu<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data is available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr577","type":"journal-article","created":{"date-parts":[[2011,10,18]],"date-time":"2011-10-18T04:27:59Z","timestamp":1318912079000},"page":"3430-3431","source":"Crossref","is-referenced-by-count":118,"title":["Enrich: software for analysis of protein function by enrichment and depletion of variants"],"prefix":"10.1093","volume":"27","author":[{"given":"Douglas M.","family":"Fowler","sequence":"first","affiliation":[{"name":"1 Department of Genome Sciences, 2Howard Hughes Medical Institute and 3Department of Medicine, University of Washington, Seattle, WA 98195, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carlos L.","family":"Araya","sequence":"additional","affiliation":[{"name":"1 Department of Genome Sciences, 2Howard Hughes Medical Institute and 3Department of Medicine, University of Washington, Seattle, WA 98195, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wayne","family":"Gerard","sequence":"additional","affiliation":[{"name":"1 Department of Genome Sciences, 2Howard Hughes Medical Institute and 3Department of Medicine, University of Washington, Seattle, WA 98195, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stanley","family":"Fields","sequence":"additional","affiliation":[{"name":"1 Department of Genome Sciences, 2Howard Hughes Medical Institute and 3Department of Medicine, University of Washington, Seattle, WA 98195, USA"},{"name":"1 Department of Genome Sciences, 2Howard Hughes Medical Institute and 3Department of Medicine, University of Washington, Seattle, WA 98195, USA"},{"name":"1 Department of Genome Sciences, 2Howard Hughes Medical Institute and 3Department of Medicine, University of Washington, Seattle, WA 98195, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2011,10,17]]},"reference":[{"key":"2023012511295302000_B1","doi-asserted-by":"crossref","first-page":"1565","DOI":"10.1126\/science.1131969","article-title":"Engineering yeast transcription machinery for improved ethanol tolerance and production","volume":"314","author":"Alper","year":"2006","journal-title":"Science"},{"key":"2023012511295302000_B2","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1016\/j.tibtech.2011.04.003","article-title":"Deep mutational scanning: assessing protein function on a massive scale","volume":"29","author":"Araya","year":"2011","journal-title":"Trends Biotechnol."},{"key":"2023012511295302000_B3","doi-asserted-by":"crossref","first-page":"1767","DOI":"10.1093\/nar\/gkp1137","article-title":"The Sanger FASTQ file format for sequences with quality scores, and the Solexa\/Illumina FASTQ variants","volume":"38","author":"Cock","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023012511295302000_B4","doi-asserted-by":"crossref","first-page":"e110","DOI":"10.1093\/nar\/gkq052","article-title":"Rapid interactome profiling by massive sequencing","volume":"38","author":"Di Niro","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023012511295302000_B5","doi-asserted-by":"crossref","first-page":"e8338","DOI":"10.1371\/journal.pone.0008338","article-title":"Next-generation phage display: integrating and comparing available molecular tools to enable cost-effective high-throughput analysis","volume":"4","author":"Dias-Neto","year":"2009","journal-title":"PLoS One"},{"key":"2023012511295302000_B6","doi-asserted-by":"crossref","first-page":"1782","DOI":"10.1039\/c0mb00061b","article-title":"Coevolution of PDZ domain-ligand interactions analyzed by high-throughput phage display and deep sequencing","volume":"6","author":"Ernst","year":"2010","journal-title":"Mol. 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