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RepeatModeler specifications

Information


Unique identifier OMICS_19729
Name RepeatModeler
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
License Open Software License v. 2.1
Computer skills Advanced
Version 1.0.10
Stability Stable
Requirements
RepeatMasker & Libraries, RECON, RepeatScout, TRF, NSEG, RMBlast, ABBlast/WUBlast
Maintained Yes

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Versioning


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RepeatModeler citations

 (234)
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

[…] i 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 through homolog and de novo prediction. The RepeatMasker and RepeatProteinMask were used to screen the A. ipaensis ge […]

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

[…] were identified following the standard Maker-P recipe (weatherby.genetics.utah.edu/MAKER/wiki/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) MITEhu […]

library_books

Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species

2018
PLoS Biol
PMCID: 5916493
PMID: 29689044
DOI: 10.1371/journal.pbio.2004830

[…] Repetitive regions were masked prior to gene prediction. Repeats were modelled ab initio using RepeatModeler v1.0.5 []. Repeats arising from duplicated genes or recent gene family expansions (e.g., alpha-tubulin in R. magnacalcarata []) were removed from the custom repeat library by comparing e […]

library_books

Pathogenic adaptations of Colletotrichum fungi revealed by genome wide gene family evolutionary analyses

2018
PLoS One
PMCID: 5915685
PMID: 29689067
DOI: 10.1371/journal.pone.0196303

[…] generate scaffolds. The generated genome assembly was deposited at GenBank under accession no. MVNS00000000.Repetitive DNA elements were predicted with a combination of RepeatMasker version 4.0.5 and RepeatModeler version 1.0.8. To predict gene structures, Augustus version 3.1 [], SNAP version 2013-11-29 [], GeneMark-ES version 2.3c [], and MAKER2 version 2.31.8 [] were used in combination. August […]

library_books

Draft genome sequence of Camellia sinensis var. sinensis provides insights into the evolution of the tea genome and tea quality

2018
Proc Natl Acad Sci U S A
PMCID: 5939082
PMID: 29678829
DOI: 10.1073/pnas.1719622115

[…] sing methods as described in SI Appendix, section 1.4. We searched transposable elements in the tea plant genome by integrating de novo methods and homology-based methods with the prediction programs RepeatModeler (www.repeatmasker.org/RepeatModeler/), LTR_FINDER (), RepeatMasker (www.repeatmasker.org), and RepeatProteinMask (version 3.3.0; www.repeatmasker.org/RepeatProteinMask.html). Based on th […]

library_books

Inter genome comparison of the Quorn fungus Fusarium venenatum and the closely related plant infecting pathogen Fusarium graminearum

2018
BMC Genomics
PMCID: 5907747
PMID: 29673315
DOI: 10.1186/s12864-018-4612-2

[…] The assembled genome was annotated using the MAKER (version 2.30) [] annotation pipeline with RepeatMasker (version 4.0.5) []. A F. venenatum specific repeat library was constructed using RepeatModeler (version 1.0.7) and supplied to MAKER for the repeat masking step. Gene calls were generated using FGENESH (version 3.1.2) [] using the Fusarium matrix, AUGUSTUS (version 2.7) [] using F […]

Citations

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RepeatModeler funding source(s)
Supported by the NIH (R44 HG02244 and R01 HG002939) and the Institute for Systems Biology.

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