{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,21]],"date-time":"2026-04-21T21:46:57Z","timestamp":1776808017291,"version":"3.51.2"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2021,5,9]],"date-time":"2021-05-09T00:00:00Z","timestamp":1620518400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01-HG006677"],"award-info":[{"award-number":["R01-HG006677"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R35-GM130151"],"award-info":[{"award-number":["R35-GM130151"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,7,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Improvements in DNA sequencing technology and computational methods have led to a substantial increase in the creation of high-quality genome assemblies of many species. To understand the biology of these genomes, annotation of gene features and other functional elements is essential; however, for most species, only the reference genome is well-annotated.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>One strategy to annotate new or improved genome assemblies is to map or \u2018lift over\u2019 the genes from a previously annotated reference genome. Here, we describe Liftoff, a new genome annotation lift-over tool capable of mapping genes between two assemblies of the same or closely related species. Liftoff aligns genes from a reference genome to a target genome and finds the mapping that maximizes sequence identity while preserving the structure of each exon, transcript and gene. We show that Liftoff can accurately map 99.9% of genes between two versions of the human reference genome with an average sequence identity &amp;gt;99.9%. We also show that Liftoff can map genes across species by successfully lifting over 98.3% of human protein-coding genes to a chimpanzee genome assembly with 98.2% sequence identity.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Liftoff can be installed via bioconda and PyPI. In addition, the source code for Liftoff is available at https:\/\/github.com\/agshumate\/Liftoff.<\/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\/btaa1016","type":"journal-article","created":{"date-parts":[[2020,11,24]],"date-time":"2020-11-24T21:43:35Z","timestamp":1606254215000},"page":"1639-1643","source":"Crossref","is-referenced-by-count":859,"title":["Liftoff: accurate mapping of gene annotations"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4450-1857","authenticated-orcid":false,"given":"Alaina","family":"Shumate","sequence":"first","affiliation":[{"name":"Department of Biomedical Engineering, Johns Hopkins University , Baltimore, MD 21218, USA"},{"name":"Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University , Baltimore, MD 21211, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8859-7432","authenticated-orcid":false,"given":"Steven L","family":"Salzberg","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, Johns Hopkins University , Baltimore, MD 21218, USA"},{"name":"Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University , Baltimore, MD 21211, USA"},{"name":"Department of Computer Science, Johns Hopkins University , Baltimore, MD 21218, USA"},{"name":"Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University , Baltimore, MD 21205, USA"}]}],"member":"286","published-online":{"date-parts":[[2021,5,9]]},"reference":[{"key":"2023051709462735200_btaa1016-B1","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1534\/genetics.120.303501","article-title":"Chromosome-scale assembly of the bread wheat genome reveals thousands of additional gene copies","volume":"216","author":"Alonge","year":"2020","journal-title":"Genetics"},{"key":"2023051709462735200_btaa1016-B2","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1038\/nature04072","article-title":"Initial sequence of the chimpanzee genome and comparison with the human genome","volume":"437","year":"2005","journal-title":"Nature"},{"key":"2023051709462735200_btaa1016-B3","doi-asserted-by":"crossref","first-page":"e1001091","DOI":"10.1371\/journal.pbio.1001091","article-title":"Modernizing reference genome assemblies","volume":"9","author":"Church","year":"2011","journal-title":"PLoS Biol"},{"key":"2023051709462735200_btaa1016-B4","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1007\/BF01386390","article-title":"A note on two problems in connexion with graphs","volume":"1","author":"Dijkstra","year":"1959","journal-title":"Numer. 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