Repbase statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Repbase
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Tool usage distribution map

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Associated diseases

This word cloud represents Repbase usage per disease context
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Popular tool citations

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Protocols

Repbase specifications

Information


Unique identifier OMICS_03539
Name Repbase
Alternative names RU, Repbase Update
Restrictions to use Academic or non-commercial use
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Allowed
Version 21.12
Maintained Yes

Maintainers


  • person_outline Jurka J.
  • person_outline Weidong Bao
  • person_outline Kenji Kojima

Publications for Repbase

Repbase citations

 (808)
library_books

Expressed repetitive elements are broadly applicable reference targets for normalization of reverse transcription qPCR data in mice

2018
Sci Rep
PMCID: 5955877
PMID: 29769563
DOI: 10.1038/s41598-018-25389-6

[…] e identified following a slightly adapted workflow previously published for zebrafish. In a first step, 313 EREs present in the mouse genome were identified using the repetitive DNA element database, Repbase (http://www.girinst.org/repbase). Since the number of copies for the different EREs in the mouse genome was unknown in Repbase, initially 16 EREs were selected based on a mean conservation rat […]

library_books

Comparative Genomics Reveals the Core Gene Toolbox for the Fungus Insect Symbiosis

2018
MBio
PMCID: 5954228
PMID: 29764946
DOI: 10.1128/mBio.00636-18

[…] tellites, simple repeats, and low-complexity sequences were annotated with RepeatMasker v4.0.5 (http://www.repeatmasker.org) and Tandem Repeat Finder v4.07b (), corresponding to fungal sequences from RepBase (). The genomes were annotated with the Funannotate v0.6.2 pipeline (https://github.com/nextgenusfs/funannotate), employing tools of Augustus (), GeneMark.hmm-ES (), and EVM (). Gene function […]

library_books

Genome Sequencing and Analysis of the Peanut B Genome Progenitor (Arachis ipaensis)

2018
Front Plant Sci
PMCID: 5943715
PMID: 29774047
DOI: 10.3389/fpls.2018.00604

[…] ith and Hubley, ) were performed to identify repetitive sequences through homolog and de novo prediction. The RepeatMasker and RepeatProteinMask were used to screen the A. ipaensis genome against the RepBase database (http://www.girinst.org/). The transposable elements (TEs) were classified as described without consideration of the gaps in the genome assembly (Wicker et al., ). […]

library_books

Whole genome de novo sequencing reveals unique genes that contributed to the adaptive evolution of the Mikado pheasant

2018
GigaScience
PMCID: 5941149
PMID: 29722814
DOI: 10.1093/gigascience/giy044

[…] First, RepeatMasker (version 4.0.5; parameter: “-species chicken”), including rmblastn (version 2.2.23+) as the search engine, RepBase (version 20140131), and RM database (version 20140131), were applied to screen the scaffolds for interspersed repeats and low-complexity regions in the DNA sequences, and the masked genome was […]

call_split

Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen fixing rhizobium symbioses

2018
Proc Natl Acad Sci U S A
PMCID: 5960304
PMID: 29717040
DOI: 10.1073/pnas.1721395115
call_split See protocol

[…] iki/index.php/Repeat_Library_Construction-Advanced, accessed October 2015) as described on the GMOD site: (i) RepeatModeler with Repeatscout v1.0.5, Recon v1.08, RepeatMasker version open4.0.5, using RepBase version 20140131 () and TandemRepeatFinder; (ii) GenomeTools LTRharvest and LTRdigest (); (iii) MITEhunter with default parameters (). We generated species-specific repeat libraries for P. and […]

call_split

A somatic role for the histone methyltransferase Setdb1 in endogenous retrovirus silencing

2018
Nat Commun
PMCID: 5923290
PMID: 29703894
DOI: 10.1038/s41467-018-04132-9
call_split See protocol

[…] California at Santa Cruz RepeatMasker track (mm9) and we selected ERVs annotated with high SW (Smith–Waterman) probability scores (≥2000). Sequences of RepeatMasker annotated ERVs were compared with Repbase consensus sequences and scored for percentage of similarity or length mismatch. We applied SW 2000 as a cutoff because sufficient LTR only types (such as IAPLTR1a, RLTR6_Mm, or RLTR10C) could […]


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Repbase institution(s)
Genetic Information Research Institute, Los Altos, CA, USA; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan; Institute of Medical Science, University of Tokyo, Tokyo, Japan
Repbase funding source(s)
This work was supported by a grant from the National Institutes of Health (2P41 LM 006252-07A1).

Repbase review

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ravindra raut

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Dataset
Repbase is the good tool for classy and analyzing the repeats, It gives vivid information about repeats such as exact masking sequence, its length, its name and class along with the source research paper. I am using it for my research; I definitely recommend to the fellow researchers who want to do the analysis of the DNA.