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A program to identify Helitron given genomic sequences. HelSearch searches for CTRRT in genomic sequence first. To narrow the results, insertion site T was included in this search. The proposed Helitron end (helend) structure is composed of a minimum of 6 hairpin pairs (2 mismatches allowed) upstream of the CTRR, a 2- to 4-bp loop, and 5–8 bp between the hairpin and CTRR. The program was developed in PERL to search for these features in a given genome.

Software type:
Command line interface
Restrictions to use:
Operating system:
Programming languages:
Academic Free License version 3.0
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  • Lixing Yang


Department of Genetics, University of Georgia, Athens, GA 30602

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    PMID: 19622734
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    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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