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  4. Repetitive DNA
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Identifies homologous groups applicable to genome sequences that have been properly marked for low-complexity repeats and annotated interspersed repeats. HomologMiner incorporates several new methods: a new abstract definition of consistent duplicate units, a new criterion to remove moderately frequent tandem repeats, and new algorithmic techniques.

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

Department of Computer Science & Engineering, Penn State University, PA, USA

  • (Hou et al., 2007) HomologMiner: looking for homologous genomic groups in whole genomes. Bioinformatics.
    PMID: 17308341
  • (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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