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While each reference sequence is transformed into a single sequence of synteny blocks (a list of signed numbers), the assembly corresponds to multiple sequences of synteny blocks because the target genome has been fragmented into multiple contigs.
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Figure 3 shows an image of a comparison between the GRCh37 and HuRef Assemblies (Region II in the HuRef assembly corresponds to the sequence from 86,921,230 to 86,960,742 in AC_000146.1) using a dot matrix plotting program http://www.vivo.colostate.edu/molkit/dnadot/.edu/molkit/dnadot/
It is usually unknown which part of the inferred assembly corresponds to which part of the reference genome.
The Q clones in this assembly corresponded to 15% of the clones.
However, different studies have found an increased frequency of the inversion, around 60%, in populations of European ancestry, indicating that the human reference assembly corresponds to the minor allelic orientation of the region [4], [11], [12].
The unigenes in the MIRA assembly corresponded to about 60% of the protein coding genes of A. thaliana [ 47].
Together, this leads to an estimate that the wheat transcript assembly corresponds to at most ~62,000-80,000 homoeologs (assuming three homoeologs/gene).
Using the known TREP library and the de novo repeat library from this study, we determined that 76.6% of the 6BS assembly and 85.5% of the 6BL assembly correspond to repeat elements.
An intact ORF encoding a recombinase on the KB-1 plasmid assembly corresponds to a pseudogene (Glov_3699) with a 119 bp deletion on pSZ77.
Using a series of engineered metal ion trapping mutants, we showed that the more compact of the two assemblies corresponds to an arrangement populated during activation of full-length receptors.
In fact, most of the singletons obtained with the WGP physical assembly correspond to BACs that are found in the depth rather than in the length of the map.
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