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If coverage was complete, the assembled sequence was compared with the reference sequence to determine if the clone were acceptable.
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Very few of the comprehensive maps are in complete agreement with the assembled genome sequence.
The annotation of these elements was carried out in two steps: identifying a reliable set of Helitron ends under stringent conditions, and searching for complete Helitrons in the assembled genomes, using data from the previous step under relaxed settings.
However, rare species in these samples can hardly get their complete genomes, and generally the assembled genome only represents a pan-genome owing to the presence of sub-species or horizontal gene transfer events.
The length of the assembled complete MgPa operon varied from 8,434 bp to 8,506 bp (Table 1).
On average 72.1% (SD: ±14.6%) of the CEGs aligned as complete gene copies to the assembled contigs (Additional file 2), compared to 81.7% (SD: ± 9.7%) that aligned as fragmented partial gene copies (Additional file 2).
However, as these data represent expression in P. balsamifera and as this gene is not deleted in female P. trichocarpa trees (as suggested by the presence of the complete gene structure in the assembled genome sequence) these results require caution for extrapolation to the aspens.
The assembled and complete genome sequences of two strains representing the pink-pigmented facultative methylotrophs of the genus Methylobacterium reveal extensive genome-wide homology and gene synteny.
before the availability of the complete assembled soybean genome, data had indicated that the soybean genome was a mosaic of alternating homeologous regions retaining high sequence conservation and regions showing very low conservation [[ 35]].
Until recently, the complete assembled sequence of the CUP1 array was available only for S288c (Johnston et al. 1994).
The reason that the number of complete genes assembled for the simulated dataset is less than that for the real dataset is that many complete genes are already well assembled for the simulated data due to its higher sequencing depth.
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