{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:43:13Z","timestamp":1753875793837,"version":"3.41.2"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,12,29]],"date-time":"2022-12-29T00:00:00Z","timestamp":1672272000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Center for Food Safety and Applied Nutrition"},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Scientists seeking to understand the genomic basis of bacterial phenotypes, such as antibiotic resistance, today have access to an unprecedented number of complete and nearly complete genomes. Making sense of these data requires computational tools able to perform multiple-genome comparisons efficiently, yet currently available tools cannot scale beyond several tens of genomes.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We describe PRAWNS, an efficient and scalable tool for multiple-genome analysis. PRAWNS defines a concise set of genomic features (metablocks), as well as pairwise relationships between them, which can be used as a basis for large-scale genotype\u2013phenotype association studies. We demonstrate the effectiveness of PRAWNS by identifying genomic regions associated with antibiotic resistance in Acinetobacter baumannii.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>PRAWNS is implemented in C++ and Python3, licensed under the GPLv3 license, and freely downloadable from GitHub (https:\/\/github.com\/KiranJavkar\/PRAWNS.git).<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac844","type":"journal-article","created":{"date-parts":[[2022,12,28]],"date-time":"2022-12-28T22:41:03Z","timestamp":1672267263000},"source":"Crossref","is-referenced-by-count":3,"title":["PRAWNS: compact pan-genomic features for whole-genome population genomics"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1638-6625","authenticated-orcid":false,"given":"Kiran","family":"Javkar","sequence":"first","affiliation":[{"name":"Department of Computer Science, University of Maryland , College Park, MD 20742, USA"},{"name":"Joint Institute for Food Safety and Applied Nutrition, University of Maryland , College Park, MD 20740, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hugh","family":"Rand","sequence":"additional","affiliation":[{"name":"Center for Food Safety and Applied Nutrition, United States Food and Drug Administration , College Park, MD 20740, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Errol","family":"Strain","sequence":"additional","affiliation":[{"name":"Center for Veterinary Medicine, United States Food and Drug Administration , Laurel, MD 20708, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9617-5304","authenticated-orcid":false,"given":"Mihai","family":"Pop","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Maryland , College Park, MD 20742, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,12,29]]},"reference":[{"key":"2023010802584806700_btac844-B1","first-page":"e000062","article-title":"Quantitative assessment of insertion sequence impact on bacterial genome architecture","volume":"2","author":"Adams","year":"2016","journal-title":"Microb. 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