{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,9]],"date-time":"2026-06-09T15:27:05Z","timestamp":1781018825475,"version":"3.54.1"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2018,6,29]],"date-time":"2018-06-29T00:00:00Z","timestamp":1530230400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"XSEDE Startup Allocation","award":["TG-BIO160058"],"award-info":[{"award-number":["TG-BIO160058"]}]},{"name":"MED"},{"name":"Research Allocation","award":["TG-BIO160065"],"award-info":[{"award-number":["TG-BIO160065"]}]},{"name":"MRD"},{"name":"University of Arkansas Endowments"},{"name":"Bruker Professorship in Life Sciences to MRD"},{"name":"21st Century Chair in Global Climate Change Biology"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>It is a non-trivial task to identify and design capture probes (\u2018baits\u2019) for the diverse array of targeted-enrichment methods now available (e.g. ultra-conserved elements, anchored hybrid enrichment, RAD-capture). This often involves parsing large genomic alignments, followed by multiple steps of curating candidate genomic regions to optimize targeted information content (e.g. genetic variation) and to minimize potential probe dimerization and non-target enrichment.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this context, we developed MrBait, a user-friendly, generalized software pipeline for identification, design and optimization of targeted-enrichment probes across a range of target-capture paradigms. MrBait is an open-source codebase that leverages native parallelization capabilities in Python and mitigates memory usage via a relational-database back-end. Numerous filtering methods allow comprehensive optimization of designed probes, including built-in functionality that employs BLAST, similarity-based clustering and a graph-based algorithm that \u2018rescues\u2019 failed probes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Complete code for MrBait is available on GitHub (https:\/\/github.com\/tkchafin\/mrbait), and is also available with all dependencies via one-line installation using the conda package manager. Online documentation describing installation and runtime instructions can be found at: https:\/\/mrbait.readthedocs.io.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty548","type":"journal-article","created":{"date-parts":[[2018,6,29]],"date-time":"2018-06-29T03:10:31Z","timestamp":1530241831000},"page":"4293-4296","source":"Crossref","is-referenced-by-count":21,"title":["MrBait: universal identification and design of targeted-enrichment capture probes"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8687-5905","authenticated-orcid":false,"given":"Tyler K","family":"Chafin","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marlis R","family":"Douglas","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael E","family":"Douglas","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,6,29]]},"reference":[{"key":"2023012712244579700_bty548-B1","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1534\/genetics.115.183665","article-title":"RAD capture (Rapture): flexible and efficient sequence-based genotyping","volume":"202","author":"Ali","year":"2016","journal-title":"Genetics"},{"key":"2023012712244579700_bty548-B2","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. 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