REPuter pipeline

REPuter specifications

Information


Unique identifier OMICS_03541
Name REPuter
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Information


Unique identifier OMICS_03541
Name REPuter
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for REPuter

REPuter citations

 (4)
2011
PMCID: 5654404

[…] the mega software (kumar et al. 2008). identification and refinement of gene structures for annotation was aided by parallel cdna analysis. repeat sequences and microsatellites were analyzed using reputer at http://bibiserv.techfak.uni-bielefeld.de/reputer/ and msatfinder at http://www.genomics.ceh.ac.uk/msatfinder/. identification of rna candidate sites in dna and analyses and annotation […]

2009
PMCID: 2749086

[…] total hgt pool. adjacent clusters were merged., crisprs were identified using crispr finder (http://crispr.u-psud.fr/server/crisprfinder.php) while repeats larger than 35 bases were identified using reputer (kurtz et al 2001). secondary metabolite gene clusters were manually annotated as in (udwary et al 2007). cluster boundaries were predicted using previously reported gene clusters […]

2007
PMCID: 1794153

[…] (to avoid snps at the ends of contigs where sequence quality tends to be poor). a final validation step verified that the snp was from a unique region of the reference sequence using the program reputer [22]. those snps located within repetitive sequence were excluded from further analysis., detection of snps was performed using the homogenous massextend (hme) assay as per manufacturers […]

2005
PMCID: 1282333

[…] rapid adaptation, such as in the invasion of a new biological niche., crisprs were identified by three methods. arrays of exact or near-exact repeats were readily detected by repfind, a part of the reputer package [27–29]. sample sequences from known arrays were used to identify additional, smaller repeat clusters by blastn (http://blast.wustl.edu). finally, regions suspected to have few and/or […]

REPuter institution(s)
Faculty of Technology, University of Bielefeld, Bielefeld, Germany

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