Repbase Update, a database of eukaryotic repetitive elements

By Jerzy Jurka, Vladimir V. Kapitonov, Adam Pavlícek, Paul Klonowski, Oleksiy Kohany, J. Walichiewicz. Cytogenetic and Genome Research, 2005

3,298 citations recorded by the source corpus.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/61533dd9e41f20e2f5deaf22afb04c94b4071eac

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Citations in the corpus

Genome Sequence of the Pea Aphid Acyrthosiphon pisum (2010, methodology): “We then built one consensus per group with the MAFFT [118] multiple sequence alignment program and classified each consensus (1) according to BLASTER matches using TBLASTX and BLASTX [114] with the entire Repbase Update databank [119] and (2) according to the presence of structural features such as ”
A Novel CpG Island Set Identifies Tissue-Specific Methylation at Developmental Gene Loci (2008, background): “In contrast, all repetitive elements (as outlined in Repbase [58]) were found to be marginally depleted in methylated CGIs (p-value , 0.”
Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq (2013, neutral): “31 (29), the RepeatMasker (35) and SimpleRepeat (36) tracks from UCSC (37).”
Specialized piRNA Pathways Act in Germline and Somatic Tissues of the Drosophila Ovary (2009, background): “We mapped all 23–29 nt small RNAs to known piRNA clusters (Brennecke et al., 2007) and to the complete collection of D. melanogaster transposable elements (Repbase) (Jurka et al., 2005).”
The Ensembl gene annotation system (2016, methodology): “RepBase repeat libraries (60) are used for RepeatMasker, and in 2011, we started to run RepeatModeler (61) to generate our own libraries for some species that are distantly related to the well-characterized mammals, such as coelacanth.”
Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis (2013, methodology): “A recent study of Rhizophagus irregularis (but not isolate DAOM-197198) provided further evidence in favor of heterokaryosis (15), so this remains an open question.”
Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor (2006, background): “Background Repbase is the most widely used database of transposable elements, with ~5800 entries as of October 2006, representing over 40 superfamilies of DNA transposons, LTR and non-LTR retrotransposons, and endogenous retroviruses [1].”
Genome Annotation and Curation Using MAKER and MAKER-P (2014, background): “This example uses a version of MAKER installed with NCBI BLAST + , Exonerate, RepeatMasker, with optional RepBase libraries, and SNAP.”
The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes (2012, methodology): “Genomic assembly scaffolds of each genomes were masked using RepeatScout (9) and RepeatMasker (10) and the RepBase (11) library of fungal repeats.”