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HelitronScanner specifications


Unique identifier OMICS_07641
Name HelitronScanner
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Chunguang Du

Publication for HelitronScanner

HelitronScanner citations


Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

Genome Biol
PMCID: 5819176
PMID: 29458393
DOI: 10.1186/s13059-018-1392-6

[…] and therefore can lead to new gene fusions [, ]. we searched for the presence of helitrons and mules near nlrs and looked for any prevalence of these elements in mic1 nlrs. for helitrons, we used helitronscanner [] to scan the full genomes of o. sativa and b. distachyon and the nlr-containing scaffolds of t. aestivum. we found no increased prevalence of helitrons next to mic1 nlrs compared […]


Integrated regulatory network reveals the early salt tolerance mechanism of Populus euphratica

Sci Rep
PMCID: 5533726
PMID: 28754917
DOI: 10.1038/s41598-017-05240-0

[…] upstream of the degs were downloaded from biomart and subjected to online tool plantcare for the prediction of cis-regulatory elements. we also predicted the helitrons from p. trichocarpa genome via helitronscanner, and further identified deg-carried helitrons by blast between predicted helitrons and consensus sequences of identified degs. altogether we integrated the degs, tfs, micrornas, […]


Pinpointing the vesper bat transposon revolution using the Miniopterus natalensis genome

PMCID: 4971623
PMID: 27489570
DOI: 10.1186/s13100-016-0071-y

[…] this process was iterated until all de novo repeats were fully represented., beyond repeatmodeler searches, attempts were made to identify low copy number and highly divergent helitrons using helitronscanner []. helitronscanner searches the genome for 5’ and 3’ terminal sequences associated with helitrons. terminal sequences are then paired with their closest partner. those falling within […]


Mining hidden polymorphic sequence motifs from divergent plant helitrons

Mob Genet Elements
PMCID: 4588551
PMID: 26442169
DOI: 10.4161/21592543.2014.971635

[…] mainly rely on sequence alignment of conserved helitron termini or manual curation. the abundance of helitrons in genomes is still underestimated. we developed an automated and generalized tool, helitronscanner, that identified a plethora of divergent helitrons in many plant genomes. a local combinational variable approach as the key component of helitronscanner offers a more granular […]

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HelitronScanner institution(s)
Department of Biology and Molecular Biology, Montclair State University, Montclair, NJ, USA

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