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. 2020 Mar 31;11:13. doi: 10.1186/s13100-020-00208-w

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© The Author(s) 2020

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 1 — Building the UCSC Repeat Browser. a Workflow for building the UCSC Repeat Browser. Repeats are annotated on the human genome by the program RepeatMasker using a database of input sequences and repeat models from RepBase and Dfam. These genomic annotations are then mapped to representative consensuses of every repeat family (consensuses are taken directly from Dfam or built from RepeatMasker output). Genomic data (brown bars all shades) such as gene annotations or user-generated data can be “lifted” from the human genome to the Repeat Browser. b Mapping of individual L1PA5 instances to the consensus. A majority of L1PA5 sequences in the human genome only contain the 3′ end as evidenced by the coverage per base (mapping coverage) and alignments of individual instances (mapping alignments of 500 randomly selected elements)