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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

Versioning


No version available

Documentation


Publications for RelocaTE

RelocaTE citations

 (4)
library_books

Tracking the genome wide outcomes of a transposable element burst over decades of amplification

2017
Proc Natl Acad Sci U S A
PMCID: 5724284
PMID: 29158416
DOI: 10.1073/pnas.1716459114

[…] s 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 (optionā€“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 sequence […]

library_books

Use it or lose it: citations predict the continued online availability of published bioinformatics resources

2017
Nucleic Acids Res
PMCID: 5397159
PMID: 28334982
DOI: 10.1093/nar/gkx182

[…] a different URL than the one originally published. This suggests that circumstances necessitating a change in URL arise at a fairly constant rate but the probability of an author expending effort to relocate their SDAR correlates with the amount of attention they receive from the scientific community. Presumably, the citation effect is not direct (i.e. most authors are not closely monitoring cita […]

library_books

Resolving the prevalence of somatic transposition in Drosophila

2017
eLife
PMCID: 5553932
PMID: 28742021
DOI: 10.7554/eLife.28297.015

[…] pairs 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 in each o […]

library_books

Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress

2015
PLoS Genet
PMCID: 4287451
PMID: 25569788
DOI: 10.1371/journal.pgen.1004915

[…] 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 […]

Citations

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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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