REPuter protocols

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REPuter specifications

Information


Unique identifier OMICS_03541
Name REPuter
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


Add your version

Maintainer


  • person_outline Stefan Kurtz <>

Additional information


http://bibiserv2.cebitec.uni-bielefeld.de/reputer?id=reputer_manual_manual

Information


Unique identifier OMICS_03541
Name REPuter
Interface Web user interface, Application programming interface
Restrictions to use None
Input data A nuclear acid sequence.
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Stefan Kurtz <>

Additional information


http://bibiserv2.cebitec.uni-bielefeld.de/reputer?id=reputer_manual_manual

Publications for REPuter

REPuter in pipelines

 (33)
2017
PMCID: 5345388
PMID: 28286710
DOI: 10.7717/peerj.3037

[…] penta-, and hexa-nucleotides, respectively. the distribution, nucleotide composition, and polymorphism among ssrs were investigated. for long repeat sequences in five morus species, the program reputer was used to assess the number and location of all four type of forward match (f), reverse match (r), complement match (c) and palindromic match (p) (). the identity of the repeat was limited […]

2017
PMCID: 5618488
PMID: 28837061
DOI: 10.3390/ijms18091839

[…] rna editor for plants (prep) suite [] with a cutoff value of 0.8. gc content was analyzed using molecular evolutionary genetics analysis (mega v6.0, tokyo metropolitan university, tokyo, japan) []. reputer ( university of bielefeld, bielefeld, germany) [] to identify the size and location of repeat sequences, including forward, palindromic, reverse, and complement repeats in the chloroplast […]

2017
PMCID: 5713258
PMID: 29088105
DOI: 10.3390/ijms18112288

[…] with subsequent manual editing. the boundaries between the ir and sc regions of f. suspensa and six other lamiales species were compared and analyzed., the reputer program [] (available online: https://bibiserv.cebitec. uni-bielefeld.de/reputer) was used to identify repeats including forward, reverse, palindrome, and complement sequences. the length […]

2017
PMCID: 5748658
PMID: 29186778
DOI: 10.3390/genes8120340

[…] through online trnascan-se web servers []. the gene map of annotated jujube chloroplast genome was drawn by ogdraw v 1.2 online []., repeat sequences in chloroplast genomes were detected by reputer online []. we included the three types: direct, reverse, and palindromic. the constraints were set to (i) minimum repeat size of 30 bp, and (ii) 90% or greater sequence identity, based […]

2016
PMCID: 4906380
PMID: 27379132
DOI: 10.3389/fpls.2016.00843

[…] with four other cp genomes using the n. otophora annotation as reference (frazer et al., )., to identify repeat sequences, including palindromic, reverse, and direct repeats within the cp genome, reputer software was used (kurtz et al., ). the following conditions for repeat identification were used in reputer: (1) hamming distance of 3, (2) 90% or greater sequence identity, (3) and a minimum […]


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REPuter in publications

 (146)
PMCID: 5920036
PMID: 29731764
DOI: 10.3389/fpls.2018.00533

[…] genome annotator). genes that not be confirmed by dogma were recognized using blastx and orf finder. the trna genes were annotated by trnascan-se v1.21 ()., the sequences were initially scanned by reputer at a repeat length ≥20 bp with a similarity of above 90% (). sequences were further processed by the tandem repeats finder software ()., for the analysis in figure , we first constructed […]

PMCID: 5885378
PMID: 29618324
DOI: 10.1186/s12864-018-4633-x

[…] determined the four types of repeat sequences, including direct (forward), inverted (palindromic), complement and reverse repeats in the oresitrophe and mukdenia chloroplast genomes using the online reputer software with a minimum repeat size of 30 bp and sequence identity greater than 90% []. chloroplast simple sequence repeats (cpssrs) were detected using msatcommander v0.8.2 [] […]

PMCID: 5875761
PMID: 29596414
DOI: 10.1371/journal.pone.0192966

[…] using mvista [] in shuffle-lagan mode and using the p. taeda genome as a reference., repeat sequences, including direct, reverse, and palindromic repeats, were identified within the cp genome using reputer [] with the following settings: hamming distance of 3, ≥90% sequence identity, and minimum repeat size of 30 bp. furthermore, ssrs were detected using phobos version 3.3.12 [] with the search […]

PMCID: 5861152
PMID: 29593773
DOI: 10.3389/fpls.2018.00324

[…] and indels. the minimum alignment score and maximum period size were set at 50 and 500, respectively. all the identified repeats were manually verified and nested, or redundant results were removed. reputer () was employed to identify the irs in s. cusia by forward versus reverse complement (palindromic) alignment. the minimal repeat size was set at 30 bp, and the cutoff for similarities among […]

PMCID: 5846728
PMID: 29529038
DOI: 10.1371/journal.pone.0192956

[…] detected as described by chen et al. []. tandem repeats were identified by tandem repeats finder version 4.07b [] with default settings. forward repeats and palindromic repeats were determined by reputer [], with the minimum size set at 30 bp and a hamming distance of 3. simple sequence repeats (ssrs) were examined by perlscript misa2 (http://pgrc.ipk-gatersleben.de/misa/misa.html) to detect […]


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REPuter institution(s)
Faculty of Technology, University of Bielefeld, Bielefeld, Germany; Artemis Pharmaceuticals, Köln, Germany; Max Planck Institute for Molecular Genetics, Department for Computational Molecular Biology, Berlin, Germany
REPuter funding source(s)
Supported in part by grant KU 1257/1 from the Deutsche Forschungsgemeinschaft and by the DFG-Graduiertenkolleg 635 Bioinformatik.

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