Repbase Update, a database of repetitive elements in eukaryotic genomes

By Weidong Bao, K. Kojima, Oleksiy Kohany. Mobile DNA, 2015

2,684 citations recorded by the source corpus.

Repbase Update (RU) is a database of representative repeat sequences in eukaryotic genomes. Since its first development as a database of human repetitive sequences in 1992, RU has been serving as a well-curated reference database fundamental for almost all eukaryotic genome sequence analyses. Here, we introduce recent updates of RU, focusing on technical issues concerning the submission and updating of Repbase entries and will give short examples of using RU data. RU sincerely invites a broader submission of repeat sequences from the research community.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/95162f20fa22a8cfe84b74aa118f18a6f04eb1ab

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Citations in the corpus

RepeatModeler2 for automated genomic discovery of transposable element families (2020, methodology): “Classification is the only step that requires a database, and can be completed with only open-source Dfam if Repbase is not available.”
Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies (2018, methodology): “Repeat annotations were produced with Repeat-Masker [21] using RepBase version 2017-01-27 [22].”
Next-Generation Sequencing — An Overview of the History, Tools, and “Omic” Applications (2016, background): “[250] Bao W, Kojima KK, Kohany O: Repbase Update, a database of repetitive elements in eukaryotic genomes.”
A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas (2020, neutral): “(Dfam Consensus-20170127 and RepBase-20170127) [70, 71] with parameters “-s -species “Crassostrea gigas” -e ncbi”.”
tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes (2019, background): “By checking against these repetitive elements well-studied in mouse (86), we found that a fair portion of the lowestscoring tRNA predictions not categorized as pseudogenes are mostly part of the B1 or B2 repeats.”
RepeatModeler2: automated genomic discovery of transposable element families (2019, methodology): “Consensus sequences are generally stored in widely used databases such as Repbase (Bao et al. 2015) or along with seed alignments and HMMs in Dfam (Hubley et al. 2016).”
Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline (2019, methodology): “com/bioinfolabmu/GenericRepeatFinder), as well as a repeat database Repbase 176 [30], which is widely used as the default library in RepeatMasker [29].”
The Dfam database of repetitive DNA families (2015, methodology): “The entries in Dfam are designed to be a drop-in replacement for the Repbase-derived library of consensus sequences (12) used by RepeatMasker for repeat detection.”
Progressive Cactus is a multiple-genome aligner for the thousand-genome era (2020, positive): “The DISCOVAR genomes were masked with RepeatMasker commit 2d947604, using Repbase [49] version 20170127 as the repeat library and CrossMatch as the alignment engine.”
Significantly improving the quality of genome assemblies through curation (2020, neutral): “centromeres Repeatmasker [40,48] centromere db [33] x x”