{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:26Z","timestamp":1740185126454,"version":"3.37.3"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2021,9,15]],"date-time":"2021-09-15T00:00:00Z","timestamp":1631664000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["GM022778","AI136794"],"award-info":[{"award-number":["GM022778","AI136794"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000011","name":"Howard Hughes Medical Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000011","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Yale University and by the National Institutes of Health","award":["S10RR029676"],"award-info":[{"award-number":["S10RR029676"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Recent efforts to identify novel bacterial structured noncoding RNA (ncRNA) motifs through searching long, GC-rich intergenic regions (IGRs) have revealed several new classes, including the recently validated HMP-PP riboswitch. The DIMPL (Discovery of Intergenic Motifs PipeLine) discovery pipeline described herein enables rapid extraction and selection of bacterial IGRs that are enriched for structured ncRNAs. Moreover, DIMPL automates the subsequent computational steps necessary for their functional identification.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The DIMPL pipeline is freely available as a Docker image with an accompanying set of Jupyter notebooks. Full instructions for download and use are available at https:\/\/github.com\/breakerlab\/dimpl.<\/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\/btab624","type":"journal-article","created":{"date-parts":[[2021,9,10]],"date-time":"2021-09-10T19:10:14Z","timestamp":1631301014000},"page":"533-535","source":"Crossref","is-referenced-by-count":2,"title":["DIMPL: a bioinformatics pipeline for the discovery of structured noncoding RNA motifs in bacteria"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4030-0254","authenticated-orcid":false,"given":"Kenneth I","family":"Brewer","sequence":"first","affiliation":[{"name":"Department of Molecular Biophysics and Biochemistry, Yale University , New Haven, CT 06520-8103, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Glenn J","family":"Gaffield","sequence":"additional","affiliation":[{"name":"Howard Hughes Medical Institute, Yale University , New Haven, CT 06520-8103, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Malavika","family":"Puri","sequence":"additional","affiliation":[{"name":"Department of Molecular, Cellular and Developmental Biology, Yale University , New Haven, CT 06520-8103, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ronald R","family":"Breaker","sequence":"additional","affiliation":[{"name":"Department of Molecular Biophysics and Biochemistry, Yale University , New Haven, CT 06520-8103, USA"},{"name":"Howard Hughes Medical Institute, Yale University , New Haven, CT 06520-8103, USA"},{"name":"Department of Molecular, Cellular and Developmental Biology, Yale University , New Haven, CT 06520-8103, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,9,15]]},"reference":[{"key":"2023020108415515800_btab624-B1","doi-asserted-by":"crossref","first-page":"D7","DOI":"10.1093\/nar\/gkv1290","article-title":"Database resources of the National Center for Biotechnology Information","volume":"44","author":"Agarwala","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023020108415515800_btab624-B2","doi-asserted-by":"crossref","first-page":"e45210","DOI":"10.7554\/eLife.45210","article-title":"A bacterial riboswitch class for the thiamin precursor HMP-PP employs a terminator-embedded aptamer","volume":"8","author":"Atilho","year":"2019","journal-title":"eLife"},{"key":"2023020108415515800_btab624-B3","doi-asserted-by":"crossref","first-page":"867","DOI":"10.1016\/j.molcel.2011.08.024","article-title":"Prospects for riboswitch discovery and analysis","volume":"43","author":"Breaker","year":"2011","journal-title":"Mol. 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