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RepeatScout specifications

Information


Unique identifier OMICS_03540
Name RepeatScout
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Version 1.0.5
Stability Stable
Maintained Yes

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Documentation


Publication for RepeatScout

RepeatScout citations

 (152)
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

[…] lowing 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) MITEhunter with default p […]

library_books

Comparative genomics of the wheat fungal pathogen Pyrenophora tritici repentis reveals chromosomal variations and genome plasticity

2018
BMC Genomics
PMCID: 5913888
PMID: 29685100
DOI: 10.1186/s12864-018-4680-3

[…] osable elements using RepeatMasker (RM) [] version open-4.0.6 with rmblastn version 2.2.27+ on RepBase [] RM database version 20,150,807 (taxon = fungi). De novo repeat families were identified using RepeatScout version 1.0.5 []. LTR regions were identified using GenomeTools, Suffixerator, LTRHarvest (GenomeTools) v1.5.1 (minimum distance 200 bp and maximum distance 5000) and LTRDigest (GenomeTool […]

library_books

Intraspecific comparative genomics of isolates of the Norway spruce pathogen (Heterobasidion parviporum) and identification of its potential virulence factors

2018
BMC Genomics
PMCID: 5870257
PMID: 29580224
DOI: 10.1186/s12864-018-4610-4

[…] TEs in reference assembly were predicted using RepeatScout v.1.0.5 [], Nseg [], TRF [] and classified with REPCLASS v.1.0.1 [] and tblastx against Repbase Update database v.29.8.2016. Full-length long terminal repeat (LTR) retrotransposons were id […]

library_books

The Most Developmentally Truncated Fishes Show Extensive Hox Gene Loss and Miniaturized Genomes

2018
Genome Biol Evol
PMCID: 5906920
PMID: 29684203
DOI: 10.1093/gbe/evy058

[…] ndividually using the “–contain” setting.Species-specific repeat libraries were created for all eight species used in the comparative analysis using RepeatModeler () (v. 1.0.8). As RepeatModeler runs RepeatScout on only a small fragment of the assemblies (40 kB), we aimed to direct the repeat searches to the best part of each genome in order to get as complete repeat structures as possible. Thus, […]

library_books

Superior ab initio identification, annotation and characterisation of TEs and segmental duplications from genome assemblies

2018
PLoS One
PMCID: 5851578
PMID: 29538441
DOI: 10.1371/journal.pone.0193588

[…] peatModeler/), REPET [], Red [] and PILER []. RepeatModeler (RMD) is a de novo package that has been widely used for repeat identification and modeling that combines different programs: RepeatMasker, RepeatScout [], RECON [] and TRF (Tandem Repeat Finder) []. RepeatMasker identifies and masks interspersed repeats using curated libraries of consensus sequences supported by Dfam; Dfam contains entri […]

library_books

Comprehensive analysis of small RNAs expressed in developing male strobili of Cryptomeria japonica

2018
PLoS One
PMCID: 5846777
PMID: 29529051
DOI: 10.1371/journal.pone.0193665

[…] C. japonica sRNAs are listed in . Because the whole genome sequence is not yet available, the repetitive sequences of C. japonica were deduced from 1,185 contigs from 159 genomic BAC clones, by using RepeatScout [] and LTR_finder [] with default settings (). The BAC clones were derived from materials unrelated to ‘Toyama-1’ []. The predicted repeat sequences were compared with other plant repeat s […]

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RepeatScout institution(s)
Department of Computer Science and Engineering, University of California San Diego La Jolla, CA, USA

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