{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,17]],"date-time":"2026-03-17T07:04:30Z","timestamp":1773731070703,"version":"3.50.1"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2020,4,4]],"date-time":"2020-04-04T00:00:00Z","timestamp":1585958400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Marine S&T Fund","award":["2018SDKJ0406-1"],"award-info":[{"award-number":["2018SDKJ0406-1"]}]},{"DOI":"10.13039\/100000001","name":"NSF","doi-asserted-by":"publisher","award":["ABI-1759906 2018"],"award-info":[{"award-number":["ABI-1759906 2018"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Programmed DNA elimination (PDE) plays a crucial role in the transitions between germline and somatic genomes in diverse organisms ranging from unicellular ciliates to multicellular nematodes. However, software specific for the detection of DNA splicing events is scarce. In this paper, we describe Accurate Deletion Finder (ADFinder), an efficient detector of PDEs using high-throughput sequencing data. ADFinder can predict PDEs with relatively low sequencing coverage, detect multiple alternative splicing forms in the same genomic location and calculate the frequency for each splicing event. This software will facilitate research of PDEs and all down-stream analyses.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>By analyzing genome-wide DNA splicing events in two micronuclear genomes of Oxytricha trifallax and Tetrahymena thermophila, we prove that ADFinder is effective in predicting large scale PDEs.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The source codes and manual of ADFinder are available in our GitHub website: https:\/\/github.com\/weibozheng\/ADFinder.<\/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\/btaa226","type":"journal-article","created":{"date-parts":[[2020,3,31]],"date-time":"2020-03-31T11:12:59Z","timestamp":1585653179000},"page":"3632-3636","source":"Crossref","is-referenced-by-count":16,"title":["ADFinder: accurate detection of programmed DNA elimination using NGS high-throughput sequencing data"],"prefix":"10.1093","volume":"36","author":[{"given":"Weibo","family":"Zheng","sequence":"first","affiliation":[{"name":"Institute of Evolution & Marine Biodiversity , Ocean University of China, Qingdao 266003, China"}]},{"given":"Jing","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Mechanic and Electronic Engineering , Beijing Information Science & Technology University, Beijing 100192, China"}]},{"given":"Thomas G","family":"Doak","sequence":"additional","affiliation":[{"name":"Department of Biology , Indiana University"},{"name":"National Center for Genome Assembly Support , Indiana University, Bloomington, IN 47401, USA"}]},{"given":"Weibo","family":"Song","sequence":"additional","affiliation":[{"name":"Institute of Evolution & Marine Biodiversity , Ocean University of China, Qingdao 266003, China"},{"name":"Laboratory for Marine Biology and Biotechnology , Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China"}]},{"given":"Ying","family":"Yan","sequence":"additional","affiliation":[{"name":"Institute of Evolution & Marine Biodiversity , Ocean University of China, Qingdao 266003, China"}]}],"member":"286","published-online":{"date-parts":[[2020,4,4]]},"reference":[{"key":"2023070101190578500_btaa226-B1","first-page":"236","article-title":"What is next generation sequencing?","volume":"98","author":"Behjati","year":"2013","journal-title":"Arch. 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