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RelocaTE specifications

Information


Unique identifier OMICS_03506
Name RelocaTE
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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Publications for RelocaTE

RelocaTE in publications

 (4)
PMCID: 5724284
PMID: 29158416
DOI: 10.1073/pnas.1716459114

[…] were identified using paired-end reads and relocatev1-0-2 () to classify sites as shared between the heg4/eg4 pair or the a119/a123 pair or as private. te positions in msu7 were also computed using relocate (option–reference_ins 1). because all mpings are virtually identical, relocate was run with the requirement of a minimum of 10-bp perfect alignment of the read to the te. due to high […]

PMCID: 5553932
PMID: 28742021
DOI: 10.7554/eLife.28297.015

[…] in paired-end sequencing data, where one read maps onto a mobile element, and the other is used to determine the location of the insertion in the genome (e.g. tebreak [], t-lex [], retroseq [], relocate [], temp []). since we used temp in our previous study (), we used it again here. we first validated our new sequencing data and the utility of temp by mapping transposon insertions […]

PMCID: 4287451
PMID: 25569788
DOI: 10.1371/journal.pgen.1004915

[…] model and the stress assembled transcript starts near or within the te would provide evidence that the te is acting as a promoter., nonreference te insertions were detected for oh43 and mo17 using relocate , whole genome sequence from the ncbi sra (oh43: srr447831-srr447847; mo17: srr447948-srr447950), and consensus te sequences from the maize te database . reads containing tes were identified […]

PMCID: 4154752
PMID: 25188499
DOI: 10.1371/journal.pone.0106689

[…] such as tes is fundamental to the study of genome evolution, as repeats affect genome size structure, as well as genome function , , –. several tools (e.g. t-lex2 , retroseq , tea , ngs_te_mapper , relocate , retroseq , popoolation te , te-locate ) are currently available for discovery and annotation of te sequences in high-throughput sequencing data. however, because these tools depend […]


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RelocaTE institution(s)
Department of Plant Pathology & Microbiology, University of California, Riverside, CA, USA; Institute for Integrative Genome Biology, University of California, Riverside, CA, USA; Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
RelocaTE funding source(s)
This work was supported by US National Science Foundation: IOS-1027542, W. M. Keck Foundation, Howard Hughes Medical Institute: 52008110, US Department of Agriculture: 2013-38422-20955.

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