REPuter protocols

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

 (15)
2016
PMCID: 5630911
PMID: 27503298
DOI: 10.1093/gbe/evw190

[…] group i (gi) and group ii (gii) introns is given., non-overlapping repeat elements were mapped on each genome with repeatmasker using as input sequences the repeats of at least 30 bp identified with reputer., unlike the ulva mtdnas whose genes are all encoded on the same dna strand (melton et al. 2015; melton and lopez-bautista 2016; zhou et al. 2016a, 2016b), the gloeotilopsis […]

2015
PMCID: 4366305
PMID: 25790308
DOI: 10.1371/journal.pone.0116466

[…] when genes were predicted by at least two methods. non-coding regions and rrna genes were identified manually using blast search and alignment with other reference sequences., we utilized the reputer [55] and tandem repeat finder programs [56] to screen for dispersed and tandem repeats. direct (forward), inverted (palindrome) and reverse repeats were composed of dispersed repeats, […]

2013
PMCID: 3640096
PMID: 23638113
DOI: 10.1371/journal.pone.0062548

[…] polysticta and other asterids by setting the minimum number of repeats to 10, 5, 4, 3, 3 and 3 for mono-, di-, tri, tetra-, penta- and hexanucleotides. for tandem and dispersed repeats, the program reputer [50] was used to identify these elements with a repeat unit of at least 26 bp and sequence identity greater than 90%., we used plastome genes to reconstruct a phylogeny of asterids […]

2012
PMCID: 3360038
PMID: 22655034
DOI: 10.1371/journal.pone.0037164

[…] based on a bayesian algorithm according to the bioscope software user guide., we identified repetitive sequences, including forward, palindromic, reverse, and complemented repeats, using the reputer (version 2.74; with a minimal length of 50 bp and 3 mismatches) [63]. we removed overlapped repeats manually and obtained information on tandem repeats using a tandem repeat finder […]

2012
PMCID: 3526173
PMID: 22955231
DOI: 10.1038/ismej.2012.90

[…] methods with no significant blastp matches in the non-redundant sequence databases as of july 2011 constitute 35% of the genome. these regions did not appear to be repetitive when searched using the reputer (kurtz and schleiermacher, 1999) and mummer (kurtz et al., 2004) packages. several of these predicted hypothetical coding sequences are found in pairs in the genome. of these pairs, five […]

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.

REPuter reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review REPuter