{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T04:55:10Z","timestamp":1775624110811,"version":"3.50.1"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2023,3,2]],"date-time":"2023-03-02T00:00:00Z","timestamp":1677715200000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["104111\/Z\/14\/Z"],"award-info":[{"award-number":["104111\/Z\/14\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["218288\/Z\/19\/Z"],"award-info":[{"award-number":["218288\/Z\/19\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Annotation of nonmodel organisms is an open problem, especially the detection of untranslated regions (UTRs). Correct annotation of UTRs is crucial in transcriptomic analysis to accurately capture the expression of each gene yet is mostly overlooked in annotation pipelines. Here we present peaks2utr, an easy-to-use Python command line tool that uses the UTR enrichment of single-cell technologies, such as 10\u00d7 Chromium, to accurately annotate 3\u2032 UTRs for a given canonical annotation.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>peaks2utr is implemented in Python 3 (\u22653.8). It is available via PyPI at https:\/\/pypi.org\/project\/peaks2utr and GitHub at https:\/\/github.com\/haessar\/peaks2utr. It is licensed under GNU GPLv3.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad112","type":"journal-article","created":{"date-parts":[[2023,3,1]],"date-time":"2023-03-01T17:38:41Z","timestamp":1677692321000},"source":"Crossref","is-referenced-by-count":19,"title":["peaks2utr: a robust Python tool for the annotation of 3\u2032 UTRs"],"prefix":"10.1093","volume":"39","author":[{"given":"William","family":"Haese-Hill","sequence":"first","affiliation":[{"name":"School of Infection & Immunity, MVLS, University of Glasgow , Glasgow G12 8TA, United Kingdom"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9310-4762","authenticated-orcid":false,"given":"Kathryn","family":"Crouch","sequence":"additional","affiliation":[{"name":"School of Infection & Immunity, MVLS, University of Glasgow , Glasgow G12 8TA, United Kingdom"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1246-7404","authenticated-orcid":false,"given":"Thomas D","family":"Otto","sequence":"additional","affiliation":[{"name":"School of Infection & Immunity, MVLS, University of Glasgow , Glasgow G12 8TA, United Kingdom"}]}],"member":"286","published-online":{"date-parts":[[2023,3,2]]},"reference":[{"key":"2023031117554950700_","doi-asserted-by":"crossref","first-page":"5268","DOI":"10.1038\/s41467-021-25607-2","article-title":"Single-cell transcriptomic analysis of bloodstream Trypanosoma brucei reconstructs cell cycle progression and developmental quorum sensing","volume":"12","author":"Briggs","year":"2021","journal-title":"Nat Commun"},{"key":"2023031117554950700_","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"Gigascience"},{"key":"2023031117554950700_","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1186\/1471-2105-12-491","article-title":"MAKER2: an annotation pipeline and genome-database 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Biol"},{"key":"2023031117554950700_","doi-asserted-by":"crossref","DOI":"10.3389\/fgene.2018.00671","article-title":"UTRme: a scoring-based tool to annotate untranslated regions in trypanosomatid genomes","volume":"9","author":"Rad\u00edo","year":"2018","journal-title":"Front Genet"},{"key":"2023031117554950700_","doi-asserted-by":"crossref","first-page":"2270","DOI":"10.1038\/s41467-022-30017-z","article-title":"Leveraging omic features with F3UTER enables identification of unannotated","volume":"13","author":"Sethi","year":"2022","journal-title":"Nat Commun"},{"key":"2023031117554950700_","doi-asserted-by":"crossref","first-page":"W29","DOI":"10.1093\/nar\/gkw292","article-title":"Companion: a web server for annotation and analysis of parasite genomes","volume":"44","author":"Steinbiss","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023031117554950700_","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1016\/j.gpb.2020.02.005","article-title":"Direct comparative analyses of 10X genomics chromium and Smart-seq2","volume":"19","author":"Wang","year":"2021","journal-title":"Genomics Proteomics Bioinformatics"},{"key":"2023031117554950700_","doi-asserted-by":"crossref","first-page":"R137","DOI":"10.1186\/gb-2008-9-9-r137","article-title":"Model-based analysis of ChIP-Seq (MACS)","volume":"9","author":"Zhang","year":"2008","journal-title":"Genome 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