2001
DOI: 10.1093/nar/29.22.4633
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REPuter: the manifold applications of repeat analysis on a genomic scale

Abstract: The repetitive structure of genomic DNA holds many secrets to be discovered. A systematic study of repetitive DNA on a genomic or inter-genomic scale requires extensive algorithmic support. The REPuter program described herein was designed to serve as a fundamental tool in such studies. Efficient and complete detection of various types of repeats is provided together with an evaluation of significance and interactive visualization. This article circumscribes the wide scope of repeat analysis using applications… Show more

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Cited by 1,860 publications
(1,381 citation statements)
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References 21 publications
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“…In the first step all the repeats are identified, and in the second step repeats are clustered into various repeat classes. Other computational tools falling into the same category include RepeatMatch (Delcher et al 1999) and REPuter (Kurtz and Schleiermacher 1999;Kurtz et al 2001;Boeva et al 2006). In REPuter, it is implemented using the search engine REPfind (Kurtz and Schleiermacher 1999), which uses exact repeats as seeds, and approximate repeats are predicted allowing mismatches, insertions and deletions.…”
Section: Mining Tools Based On Dictionary Approachmentioning
confidence: 99%
See 1 more Smart Citation
“…In the first step all the repeats are identified, and in the second step repeats are clustered into various repeat classes. Other computational tools falling into the same category include RepeatMatch (Delcher et al 1999) and REPuter (Kurtz and Schleiermacher 1999;Kurtz et al 2001;Boeva et al 2006). In REPuter, it is implemented using the search engine REPfind (Kurtz and Schleiermacher 1999), which uses exact repeats as seeds, and approximate repeats are predicted allowing mismatches, insertions and deletions.…”
Section: Mining Tools Based On Dictionary Approachmentioning
confidence: 99%
“…As most of the repeats are rendered imperfect by frequent point mutations, the contemporary research is oriented towards increasing the efficiency of detection of such repeats. Besides that, a good software or tool is expected to provide efficiency, flexibility, visualization and compositionality in identification and analysis of repeats (Kurtz et al 2001). Recently, handling of redundancy has also been recognized as a useful property in a good microsatellite finding tool (Reneker et al 2004).…”
Section: Outputmentioning
confidence: 99%
“…Transmembrane domains (TMs) were predicted using TMHMM 2.0 (http://www.cbs.dtu.dk/ services/TMHMM-2.0) and the DAS-TM filter server (http://mendel.imp.univie.ac.at/sat/DAS) [28]. Repetitive DNA sequences were detected using REPuter and the Tandem Repeats Finder [29,30]. The complete genome was scanned for miRNA coding regions using VMir [31], and possible miRNA coding sequences were further analyzed using MiPred [32] and RNAfold server (http://rna.…”
mentioning
confidence: 99%
“…All these techniques are used to construct the multiple alignment of periods; and they are based either on performing the pairwise alignment of periods, followed by the subsequent creation of a guide tree, or on the search for embryos or common words in periods. Thereafter, the initial multiple alignment of periods is provided; and the optimization thereof is carried out in one way or another, including the use of hidden Markov models, iterative procedures, and some other techniques [10][11][12]. However, all the developed approaches do not ensure construction of the multiple alignment, if the statistically significant pair alignment is missing in the analyzed sequences.…”
Section: Introductionmentioning
confidence: 99%