{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,14]],"date-time":"2026-03-14T03:00:31Z","timestamp":1773457231538,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2018,9,8]],"date-time":"2018-09-08T00:00:00Z","timestamp":1536364800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Institute of Information Science, Academia Sinica and the Ministry of Science and Technology","award":["MOST 106-2811-E-001-005"],"award-info":[{"award-number":["MOST 106-2811-E-001-005"]}]},{"name":"Institute of Information Science, Academia Sinica and the Ministry of Science and Technology","award":["MOST 105-2221-E-001-029-MY3"],"award-info":[{"award-number":["MOST 105-2221-E-001-029-MY3"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,4,15]]},"abstract":"Abstract<\/jats:title>\n \n Summary<\/jats:title>\n In higher eukaryotes, the generation of transcript isoforms from a single gene through alternative splicing (AS) and alternative transcription (AT) mechanisms increases functional and regulatory diversities. Annotating these alternative transcript events is essential for genomic studies. However, there are no existing tools that generate comprehensive annotations of all these alternative transcript events including both AS and AT events. In the present study, we develop CATANA, with the encoded exon usage patterns based on the flattened gene model, to identify ten types of AS and AT events. We demonstrate the power and versatility of CATANA by showing greater depth of annotations of alternative transcript events according to either genome annotation or RNA-seq data.<\/jats:p>\n <\/jats:sec>\n \n Availability and implementation<\/jats:title>\n CATANA is available on https:\/\/github.com\/shiauck\/CATANA.<\/jats:p>\n <\/jats:sec>\n \n Supplementary information<\/jats:title>\n Supplementary data are available at Bioinformatics online.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty795","type":"journal-article","created":{"date-parts":[[2018,9,6]],"date-time":"2018-09-06T11:51:26Z","timestamp":1536234686000},"page":"1414-1415","source":"Crossref","is-referenced-by-count":7,"title":["CATANA: a tool for generating comprehensive annotations of alternative transcript events"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0883-8660","authenticated-orcid":false,"given":"Cheng-Kai","family":"Shiau","sequence":"first","affiliation":[{"name":"Institute of Information Science Academia Sinica, Taipei, Taiwan"},{"name":"Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan"},{"name":"Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5910-5419","authenticated-orcid":false,"given":"Jia-Hsin","family":"Huang","sequence":"additional","affiliation":[{"name":"Institute of Information Science Academia Sinica, Taipei, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4200-8137","authenticated-orcid":false,"given":"Huai-Kuang","family":"Tsai","sequence":"additional","affiliation":[{"name":"Institute of Information Science Academia Sinica, Taipei, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,9,8]]},"reference":[{"key":"2023012808141830600_bty795-B1","doi-asserted-by":"crossref","first-page":"1304","DOI":"10.15252\/embr.201541476","article-title":"Ubiquitously expressed genes participate in cell-specific functions via alternative promoter usage","volume":"17","author":"Feng","year":"2016","journal-title":"EMBO Rep"},{"key":"2023012808141830600_bty795-B2","doi-asserted-by":"crossref","first-page":"188","DOI":"10.12688\/f1000research.2-188.v1","article-title":"Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues","volume":"2","author":"Florea","year":"2013","journal-title":"F1000Research"},{"key":"2023012808141830600_bty795-B3","doi-asserted-by":"crossref","first-page":"e1006464","DOI":"10.1371\/journal.pgen.1006464","article-title":"Alternative splicing within and between Drosophila species, sexes, tissues, and developmental stages","volume":"12","author":"Gibilisco","year":"2016","journal-title":"PLoS Genet"},{"key":"2023012808141830600_bty795-B4","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1038\/nmeth.1528","article-title":"Analysis and design of RNA sequencing experiments for identifying isoform regulation","volume":"7","author":"Katz","year":"2010","journal-title":"Nat. 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