HelitronScanner statistics

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Citations per year

Number of citations per year for the bioinformatics software tool HelitronScanner
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Tool usage distribution map

This map represents all the scientific publications referring to HelitronScanner per scientific context
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Protocols

HelitronScanner specifications

Information


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

Versioning


No version available

Documentation


Maintainer


  • person_outline Chunguang Du

Publication for HelitronScanner

HelitronScanner citations

 (4)
library_books

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

2018
Genome Biol
PMCID: 5819176
PMID: 29458393
DOI: 10.1186/s13059-018-1392-6

[…] nverted into an HMM using HMMER3 [] (Additional file ). The resulting HMM was scanned against the TREP database [] (http://botserv2.uzh.ch/kelldata/trep-db/index.html).Helitrons were identified using HelitronScanner [] with default parameters against the full genomes of O. sativa, B. distachyon, and the NLR-containing scaffolds of T. aestivum. We then converted the coordinates of Helitrons predict […]

call_split

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

2017
Sci Rep
PMCID: 5533726
PMID: 28754917
DOI: 10.1038/s41598-017-05240-0
call_split See protocol

[…] 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, and He […]

library_books

The unique genomic landscape surrounding the EPSPS gene in glyphosate resistant Amaranthus palmeri: a repetitive path to resistance

2017
BMC Genomics
PMCID: 5240378
PMID: 28095770
DOI: 10.1186/s12864-016-3336-4

[…] l signatures with the Interproscan v5.7-48 tool []. Repetitive and low complexity sequence was identified with the RepeatMasker software v4.0.6 []. Putative helitron sequences were predicted with the HelitronScanner software [] with an LCV score of 3 for both the Head and Tail scans. A self-alignment of the reference EPSPS cassette sequence was performed with the nucmer module of the Mummer v3.22 […]

call_split

Pinpointing the vesper bat transposon revolution using the Miniopterus natalensis genome

2016
Mob DNA
PMCID: 4971623
PMID: 27489570
DOI: 10.1186/s13100-016-0071-y
call_split See protocol

[…] n rounds. 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 […]


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

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