{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:07Z","timestamp":1772138047507,"version":"3.50.1"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2021,9,6]],"date-time":"2021-09-06T00:00:00Z","timestamp":1630886400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"NSF","doi-asserted-by":"publisher","award":["1158346"],"award-info":[{"award-number":["1158346"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004189","name":"Max Planck Society","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004189","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,11,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Ciliates are single-celled eukaryotes that eliminate specific, interspersed DNA sequences (internally eliminated sequences, IESs) from their genomes during development. These are challenging to annotate and assemble because IES-containing sequences are typically much less abundant in the cell than those without, and IES sequences themselves often contain repetitive and low-complexity sequences. Long-read sequencing technologies from Pacific Biosciences and Oxford Nanopore have the potential to reconstruct longer IESs than has been possible with short reads but require a different assembly strategy. Here we present BleTIES, a software toolkit for detecting, assembling, and analyzing IESs using mapped long reads.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>BleTIES is implemented in Python 3. Source code is available at https:\/\/github.com\/Swart-lab\/bleties (MIT license) and also distributed via Bioconda.<\/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\/btab613","type":"journal-article","created":{"date-parts":[[2021,9,6]],"date-time":"2021-09-06T13:49:18Z","timestamp":1630936158000},"page":"3929-3931","source":"Crossref","is-referenced-by-count":8,"title":["BleTIES: annotation of natural genome editing in ciliates using long read sequencing"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1878-4363","authenticated-orcid":false,"given":"Brandon K B","family":"Seah","sequence":"first","affiliation":[{"name":"Max Planck Institute for Developmental Biology , T\u00fcbingen 72076, Germany"}]},{"given":"Estienne C","family":"Swart","sequence":"additional","affiliation":[{"name":"Max Planck Institute for Developmental Biology , T\u00fcbingen 72076, Germany"}]}],"member":"286","published-online":{"date-parts":[[2021,9,6]]},"reference":[{"key":"2024022216311712900_btab613-B1","doi-asserted-by":"crossref","first-page":"e1002984","DOI":"10.1371\/journal.pgen.1002984","article-title":"The Paramecium germline genome provides a niche for intragenic parasitic DNA: evolutionary dynamics of internal eliminated sequences","volume":"8","author":"Arnaiz","year":"2012","journal-title":"PLoS Genet"},{"key":"2024022216311712900_btab613-B2","doi-asserted-by":"crossref","first-page":"a017764","DOI":"10.1101\/cshperspect.a017764","article-title":"Epigenetics of ciliates","volume":"5","author":"Chalker","year":"2013","journal-title":"Cold Spring Harb. 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