RepeatMasker pipeline

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

Download


Versioning


Add your version

Maintainer


  • person_outline RepeatMasker <>

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

Maintainer


  • person_outline RepeatMasker <>

RepeatMasker IN pipelines

 (218)
2018
PMCID: 5755439
PMID: 29304732
DOI: 10.1186/s12864-017-4421-z

[…] genes were confirmed by using blast+ (version 2.2.31) against the ncbi non-redundant database (nr) with an e-value cutoff of 1e−5. dispersed repeated sequences were predicted with the software of repeatmasker through aligning the genome sequence with repeat databases (eg. repbase); tandem repeats (tr) were searched via trf (tandem repeats finder). trs were first modelled by percentage […]

2018
PMCID: 5803254
PMID: 29416032
DOI: 10.1038/s41467-018-03016-2

[…] calculated as q = −10×log10(total length of variants / total length of sites (dp >3))33,34. only biallelic variants were considered for quality validation. assemblies were repeat masked using repeatmasker24. kbs-mac-74 specific centromere (158 and 178 bp monomers) and rdna (26s, 5.8s, 18s, and 5s) repeats were identified in the pbfal assembly with blast (blastn) using representative […]

2018
PMCID: 5829208
PMID: 29445022
DOI: 10.1098/rspb.2017.2732

[…] diversity per contig and bi-allelic snp frequency distribution., for both of these sequence-based methods, only putative coding regions were used to avoid noise. contigs were first masked using repeatmasker version 4.0 [31], before blastx [32] was used to identify coding regions using default parameters and the nr (non-redundant protein sequences) database. raw reads for all species […]

2018
PMCID: 5889037
PMID: 29365169
DOI: 10.1093/molbev/msy010

[…] created using the hard-masked sequences available from the ucsc genome browser. for african green monkey, the refseq chlorocebus sabaeus assembly (accession gcf_000409795.2) was hard-masked using repeatmasker annotations available from refseq. the s. pombe assembly (asm294v2) was downloaded from pombase (mcdowall et al. 2015); the s. mikatae (ifo 1815t) and s. kudriavzevii (ifo 1815t) […]

2017
PMCID: 5256215
PMID: 28082485
DOI: 10.1128/genomeA.01389-16

[…] with trnascan-se (4), rrnammer (5), and blast against the rfam (6) database, respectively, yielding 31 trna genes, two rrna operons, and six srna. ten repetitive sequences were predicted using repeatmasker (7), and six tandem repeats were analyzed using tandem repeat finder (8). furthermore, prophage and clustered regularly interspaced short palindromic repeats (crisprs) were predicted […]

RepeatMasker reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review RepeatMasker