HelSearch protocols

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HelSearch specifications


Unique identifier OMICS_09451
Name HelSearch
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
License Academic Free License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Jeffrey L. Bennetzen <>

Publication for HelSearch

HelSearch in pipeline

PMCID: 3789558
PMID: 23771679
DOI: 10.1093/dnares/dst024

[…] and m. sexta from ncbi (http://www.ncbi.nlm.nih.gov/nuccore/aixa00000000)., to identify helitrons, a series of perl scripts were written to search for helitron sequence characteristics, similar to ‘helsearch’. briefly, the method included four steps (fig. ): (i) a perl script found helitron end structures, includes hairpins, loops, and ctrrt motifs; (ii) another perl script scanned upstream […]

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HelSearch in publications

PMCID: 4683698
PMID: 26688693
DOI: 10.1186/s13100-015-0054-4

[…] have since been found in many genomes of flowering plants [, ], mosses [], fungi [–] but also many animals such as sea urchin [], fish [, ] and bats []. a recent in silico analysis using the program helsearch [] estimates the number of helitrons in rice and sorghum to approximately 7000 and 5000, respectively, covering several megabases of their hosts' genomes. the most extensively studied […]

PMCID: 4289320
PMID: 25480150
DOI: 10.1186/1471-2164-15-1071

[…] fungi to understand their origins and evolution in the fungal kingdom., we designed a pipeline for helitron identification in p. ostreatus (figure ) starting with a structure-based approach using helsearch. this approach yielded 11 and 9 putative helitron families in the pc15 and pc9 genomes, respectively (additional file : table s1). our subsequent homology-based approach uncovered another […]

PMCID: 4588551
PMID: 26442169
DOI: 10.4161/21592543.2014.971635

[…] tool looks for helitron hallmarks, including at dinucleotide insertion site, 5′-tc, ctag-3′, and a conserved 16- to 20-bp palindromic structure located 10–15 bp away from the 3′ termini. helsearch, another structure-based tool, first detects 3′ hairpins, retains those with multiple copies in the host genome, and manually extends toward 5′ ends to determine helitron 5′ boundaries. […]

PMCID: 4224331
PMID: 25223768
DOI: 10.1093/gbe/evu204

[…] of the unique transposition mechanism, long-term persistence, and propensity for gene shuffling., a complementary combination of de novo and structure-based approaches (repeatscout 1.0.2 [] and helsearch []) was employed to identify helitrons from the m. lucifugus genome (gl429767–gl433173, 3,407 scaffolds, from genbank at national center for biotechnology information [ncbi]). the repeat […]

PMCID: 4279128
PMID: 24852848
DOI: 10.1038/ncomms4930

[…] using tblastn. further upstream and downstream sequences of the candidate matches were compared with each other to define their boundaries and structure. helitron elements were identified by the helsearch 1.0 programme and manually inspected. all the te categories were identified according to the criteria described previously. typical elements of each category were selected and mixed […]

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HelSearch institution(s)
Department of Genetics, University of Georgia, Athens, GA, USA

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