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RepeatMasker specifications

Information


Unique identifier OMICS_09436
Name RepeatMasker
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTA
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Information


Unique identifier OMICS_09436
Name RepeatMasker
Interface Web user interface
Restrictions to use None
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

RepeatMasker citations

 (1996)
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

[…] c.uk/projects/fastqc/). Genomes were assembled with RAY v2.3.1 (). The scaffolds of S. simulii were built using SSPACE (). Satellites, 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 […]

library_books

NOTCH mediated non cell autonomous regulation of chromatin structure during senescence

2018
Nat Commun
PMCID: 5943456
PMID: 29743479
DOI: 10.1038/s41467-018-04283-9

[…] isplaying altered chromatin accessibility were mapped to genomic annotations or repeat regions using bedtools v2.26.0. For the genomic annotations, we used TSSs from the FANTOM database, repeats from repeatMasker (UCSC genome browser) and other genomic features (exons, introns, UTRs, etc.) were extracted from the UCSC Table Browser. The enhancers were identified based on our own H3K4me1 and H3K27a […]

library_books

Comparison of the Chinese bamboo partridge and red Junglefowl genome sequences highlights the importance of demography in genome evolution

2018
BMC Genomics
PMCID: 5941490
PMID: 29739321
DOI: 10.1186/s12864-018-4711-0

[…] omputational feasibility, the three assemblies used Kmer values of 63, 63, and 35 respectively, and we merged scaffolds with Metassembler v1.5 []. We estimated proportions of repetitive elements with RepeatMasker v4.0.5 using the “Aves” repeat library [].We annotated scaffolds with a length of 1 kb or greater using MAKER v2.31.8 [] and conducted gene predictions using AUGUSTUS v3.2.1 [] with a hid […]

library_books

Transcriptome profiling of the honeybee parasite Varroa destructor provides new biological insights into the mite adult life cycle

2018
BMC Genomics
PMCID: 5936029
PMID: 29728057
DOI: 10.1186/s12864-018-4668-z

[…] Apis mellifera and Metaseiulus occidentalis to retrieve the corresponding annotations. The contigs were also processed with rnammer (standard parameters, version 1.2) [] to find ribosomal genes, with repeatmasker (−engine crossmatch -gccalc -species Varroa destructor parameters, version open-4-0-3) [] to list the contained repeats and with interproscan (−-goterms –pathways parameters, version 4.8) […]

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

[…] ), pre-rRNAs were predicted using RNAmmer (Lagesen et al., ), pre-snRNAs were annotated using INFERNAL (Nawrocki et al., ) and others were also obtained by BLAST search against the Rfam database.The RepeatMasker (Chen, ), RepeatProteinMask (http://repeatmasker.org/), Tendem Repeats Finder (TRF) (Benson, ) and RepeatModeler (Smith and Hubley, ) were performed to identify repetitive sequences throu […]

library_books

Prediction of plant lncRNA by ensemble machine learning classifiers

2018
BMC Genomics
PMCID: 5930664
PMID: 29720103
DOI: 10.1186/s12864-018-4665-2

[…] characters. However, by not including transposable element information, the computational time for data preprocessing before transcript classification is significantly reduced to minutes from days as RepeatMasker is no longer needed.Features of secondary RNA structure have previously been used in other RNA classifiers, such as nRC [] and GraPPLE [], that are used to classify RNAs into functional c […]

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