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These meta-servers utilize many programs and aim to facilitate highly integrated sequence analysis.
The failure to find particles with characteristic badnavirus morphology suggests that virus DNA is present only as integrated sequence.
PlantSat, a database specialized for plant satDNA, has integrated sequence data from several resources such as NCBI and DNA Data Bank of Japan (DDBJ) [33], to provide a list of satDNA sequences for members of many plant families including Poaceae, Brassicaceae, Chenopodiaceae, Cucurbitaceae and Solanaceae [34 36], as well as many other plants.
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Polyclonal populations of cells harboring integrated sequences were selected with puromycin and tested for overexpression of FLAG-tagged LCN7.
We also took advantage of a recently published miRNA prediction tool utilizing integrated sequence-structure motifs to identify miRNA precursors (ss-motifs [ 28]).
Annotation information is then transferred to the newly integrated sequences.
These integrated sequences will be used to assemble the scaffolds in the B. rapa genome.
Such long-length NUPTs were very rare even in recently integrated sequences (0 6%; Supplementary Table S4).
Importantly though, our assay was conducted in vivo in ESCs using stably integrated sequences.
In HepG2.2.15 cells, HBV DNA is carried as chromosomally integrated sequences and episomally as relaxed circular, covalently closed form of HBV genome [ 39].
These integrated sequences might impact the observed specific expression of gh2 in AS compared to CS [see Additional files 2 and 3].
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