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RepeatExplorer specifications

Information


Unique identifier OMICS_07465
Name RepeatExplorer
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 0.9.7.8
Stability Stable
Maintained Yes

Publications for RepeatExplorer

RepeatExplorer citations

 (68)
library_books

Satellite DNA in Vicia faba is characterized by remarkable diversity in its sequence composition, association with centromeres, and replication timing

2018
Sci Rep
PMCID: 5895790
PMID: 29643436
DOI: 10.1038/s41598-018-24196-3

[…] enome. Putative satellite repeats were identified based on the properties of cluster graphs obtained by similarity-based clustering of low-pass genome sequencing Illumina reads, as implemented in the RepeatExplorer pipeline. These graphs represent the reads and their sequence similarities as nodes and connecting edges, respectively, and form globular or ring-like shapes in the case of tandem repea […]

library_books

Practical considerations for plant phylogenomics

2018
Appl Plant Sci
PMCID: 5895195
PMID: 29732268
DOI: 10.1002/aps3.1038

[…] ion can also be discerned through genome skim data. Although multiple studies have focused on the use of longer read technology such as 454 pyrosequencing (e.g., Harkess et al., ), the development of RepeatExplorer (Novák et al., ) and Transposome (Staton and Burke, ) enable short reads to be used for transposon identification (e.g., Staton and Burke, ). Using these approaches, genome skim data ar […]

library_books

A guide to sequence your favorite plant genomes

2018
Appl Plant Sci
PMCID: 5895188
PMID: 29732260
DOI: 10.1002/aps3.1030

[…] e elements in a genome can also be inferred by shotgun Illumina DNA sequencing data before assembly. Sequence reads that cover as little as 1% of the genome size can be used as input to programs like RepeatExplorer (available as a free Galaxy server at http://www.repeatexplorer.org/; Novák et al., ) or Transposome (Staton and Burke, ). Random, low‐coverage shotgun reads are clustered by nucleotide […]

library_books

The slowdown of Y chromosome expansion in dioecious Silene latifolia due to DNA loss and male specific silencing of retrotransposons

2018
BMC Genomics
PMCID: 5819184
PMID: 29458354
DOI: 10.1186/s12864-018-4547-7

[…] ic tool []. All 14 datasets were randomly sampled to represent approximately 0.015×/1C (the exact number of reads is shown in Additional file : Table S4) and 3,479,090 reads were analyzed altogether. RepeatExplorer pipeline [, ] was used for de novo repeat identification. Resulting clusters were characterized based on similarity searches against RepeatMasker libraries, user custom libraries, in bl […]

library_books

Uncovering the evolutionary history of neo XY sex chromosomes in the grasshopper Ronderosia bergii (Orthoptera, Melanoplinae) through satellite DNA analysis

2018
BMC Evol Biol
PMCID: 5767042
PMID: 29329524
DOI: 10.1186/s12862-017-1113-x

[…] paired-end reads were joined using the “fastq-join” software of the FASTX-Toolkit suit [] with default options. To search for satDNAs in the R. bergii genome, 4,702,802 joined reads were used in the RepeatExplorer pipeline [, ]. We then searched for clusters showing higher graph density, which is a typical feature of satDNAs families analysis [, ] due to tandem repeats characteristic of the seque […]

library_books

Genomic abundance and transcriptional activity of diverse gypsy and copia long terminal repeat retrotransposons in three wild sunflower species

2018
BMC Plant Biol
PMCID: 5755311
PMID: 29304730
DOI: 10.1186/s12870-017-1223-z

[…] iagen, Valencia, CA) to remove low quality sequences (PHRED scores <30) and sequences <80 bp and <40 bp, respectively. More stringent filtering of DNA-seq data was performed on account of the program RepeatExplorer [] requiring input sequences ≥ 80 bp in length for analysis. After quality filtering, chloroplast- and mitochondrial-derived sequences were identified and removed by mapping reads again […]

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RepeatExplorer institution(s)
Institute of Plant Molecular Biology, Biology Centre ASCR, České Budějovice, CZ, Czech Republic

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