REPuter: the manifold applications of repeat analysis on a genomic scale.

By Stefan Kurtz, J. V. Choudhuri, Enno Ohlebusch, C. Schleiermacher, J. Stoye, Robert Giegerich. Nucleic Acids Research, 2001

2,193 citations recorded by the source corpus.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/1519ebac3eb326eac33a024818f593242a1d5095

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Citations in the corpus

RSAT: regulatory sequence analysis tools (2008, methodology): “This program is a wrapper around the programs vmatch and mkvtree developed by Stefan Kurtz (6,7).”
A Guild of 45 CRISPR-Associated (Cas) Protein Families and Multiple CRISPR/Cas Subtypes Exist in Prokaryotic Genomes (2005, methodology): “CRISPRs were identified by three methods. Arrays of exact or near-exact repeats were readily detected by REPfind, a part of the REPuter package [”
CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats (2007, methodology): “(12) used REPﬁnd (http://bibiserv.techfak.uni-bielefeld.de/reputer/), a part of the REPuter package (22–24) and BLASTN to identify smaller repeat clusters.”
LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons (2008, methodology): “REPuter [5] (or the improved and more general software tool Vmatch [6]), RECON [7], RAP [8] and PILER [9].”
Replacing suffix trees with enhanced suffix arrays (2004, methodology): “To the best of our knowledge, Gusfield’s algorithm was first implemented in the REPuter-program [27], based on space efficient suffix trees described in [25].”
Plastid genome sequencing, comparative genomics, and phylogenomics: Current status and prospects (2010, methodology): “Several universal tools have already been adopted in certain plastid comparative genomic studies, for example, REPuter (Kurtz et al., 2001) for dealing with SDRs, GRAPPA (http://www.cs.unm.edu/m̃oret/GRAPPA/) and GRIMM (Tesler, 2002) for genome rearrangements, as well as PipMaker (Schwartz et al., 2”
CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats (2007, methodology): “Because of the impressive speed of suffix trees, they have been widely used in DNA repeat detection [23-26].”
Engineering a software tool for gene structure prediction in higher organisms (2005, background): “[14] for a description of the technical details.”
Aggressive assembly of pyrosequencing reads with mates (2008, methodology): “Table 2 presents four contig size statistics for assemblies of selected hybrid datasets, with CABOG assemblies compared with Newbler assemblies.”
Versatile and open software for comparing large genomes (2004, methodology): “This representation was also used in the repeat analysis tool REPuter [27].”
High-throughput sequence alignment using Graphics Processing Units (2007, methodology): “Consequently, suffix trees are used in several alignment algorithms, including MGA [10] and REPuter [11].”
WindowMasker: window-based masker for sequenced genomes (2006, methodology): “Such software packages include RAP (Campagna et al., 2005), also based on word counts; REPuter (Kurtz et al., 2001), based on suffix trees; FORrepeats (Lefebvre et al., 2003), based on an automaton construction ; an unnamed software package from Cold Spring Harbor Laboratory (Healy et al., 2003),…”
FastPCR Software for PCR Primer and Probe Design and Repeat Search (2009, background): “There are many papers describing algorithms for finding repeats in a string; in most cases, alignment methods for finding repeats start with a self-comparison to detect repeated sequences (Kurtz, 2000; Kurtz et al. 2001; Bao and Eddy 2002; Lefebvre et al. 2003; Campagna et al. 2005; Edgar and Myers ”