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Publications for RelocaTE
Tracking the genome wide outcomes of a transposable element burst over decades of amplification
[…] 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 (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 sequence […]
Use it or lose it: citations predict the continued online availability of published bioinformatics resources
[…] 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 […]
Resolving the prevalence of somatic transposition in Drosophila
[…] 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 […]
Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress
[…] 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 […]
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