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  4. Repetitive DNA
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Gathers C++ programs developed for transposable element search and their annotation in large eukaryotic genome sequence. The suite is composed by three programs BLASTER, MATCHER and GROUPER. The results of BLASTER can be treated further by the MATCHER and GROUPER program, but these two last programs can be also used in conjunction with other programs such as RepeatMasker, CENSOR, BLAST, BLAT, ... if their outputs are correctly formatted as a BLASTER output file (i.e. *.align).

Software type:
Suite
Interface:
Command line interface
Restrictions to use:
None
Operating system:
Unix/Linux
Programming languages:
C++
Computer skills:
Advanced
Stability:
Stable
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Institution(s)

Laboratoire Dynamique du GĂ©nome et Evolution, Institut Jacques Monod, Paris, France; Department of Genetics, University of Cambridge, Cambridge, United Kingdom

  • (Quesneville et al., 2005) Combined evidence annotation of transposable elements in genome sequences. PLoS computational biology.
    PMID: 16110336
  • Animals
  • Fungi
  • Plants
  • Protists
  • (Bergman and Quesneville, 2007) Discovering and detecting transposable elements in genome sequences. Briefings in bioinformatics.
    PMID: 17932080
  • (Anisimova et al., 2015) Statistical approaches to detecting and analyzing tandem repeats in genomic sequences. Frontiers in bioengineering and biotechnology.
    PMID: 25853125
  • (Saha et al., 2008) Empirical comparison of ab initio repeat finding programs. Nucleic acids research.
    PMID: 18287116
  • (Lerat, 2010) Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs. Heredity.
    PMID: 19935826
  • (Janicki et al., 2011) Bioinformatics and genomic analysis of transposable elements in eukaryotic genomes. Chromosome research.
    PMID: 21850457

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