REPuter: the manifold applications of repeat analysis on a genomic scale. 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 in five different areas of sequence analysis: checking fragment assemblies, searching for low copy repeats, finding unique sequences, comparing gene structures and mapping of cDNA/EST sequences.

References in zbMATH (referenced in 16 articles )

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  1. Gobonamang, Tshepo Kitso; Mpoeleng, Dimane: Counter based suffix tree for DNA pattern repeats (2020)
  2. I, Tomohiro; Köppl, Dominik: Improved upper bounds on all maximal (\alpha)-gapped repeats and palindromes (2019)
  3. Nakamura, Atsuyoshi; Takigawa, Ichigaku; Tosaka, Hisashi; Kudo, Mineichi; Mamitsuka, Hiroshi: Mining approximate patterns with frequent locally optimal occurrences (2016)
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  5. İleri, Atalay Mert; Külekci, M. Oğuzhan; Xu, Bojian: A simple yet time-optimal and linear-space algorithm for shortest unique substring queries (2015)
  6. Do, Huy Hoang; Sung, Wing Kin: Compressed directed acyclic word graph with application in local alignment (2013)
  7. He, Dan; Zhu, Xingquan; Wu, Xindong: Mining approximate repeating patterns from sequence data with gap constraints (2011)
  8. Christley, Scott; Lobo, Neil F.; Madey, Greg: Multiple organism algorithm for finding ultraconserved elements (2008) ioport
  9. Janky, Rekin’s; Van Helden, Jacques: Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution (2008) ioport
  10. Touyar, Narjiss; Schbath, Sophie; Cellier, Dominique; Dauchel, Hélène: Poisson approximation for the number of repeats in a stationary Markov chain (2008)
  11. Bland, Charles; Ramsey, Teresa L.; Sabree, Fareedah; Lowe, Micheal; Brown, Kyndall; Kyrpides, Nikos C.; Hugenholtz, Philip: CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats (2007) ioport
  12. Schatz, Michael C.; Trapnell, Cole; Delcher, Arthur L.; Varshney, Amitabh: High-throughput sequence alignment using graphics processing units (2007) ioport
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  14. Tian, Yuanyuan; Tata, Sandeep; Hankins, Richard A.; Patel, Jignesh M.: Algorithms for parallel memory: Two-level memories (2005) ioport
  15. Abouelhoda, Mohamed Ibrahim; Kurtz, Stefan; Ohlebusch, Enno: Replacing suffix trees with enhanced suffix arrays (2004)
  16. Stoye, Jens; Gusfield, Dan: Simple and flexible detection of contiguous repeats using a suffix tree (2002)