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It is the first element of the candidate assembly sequence (mathbf {C}).
The goal of the assembly planning component is to find a set of candidate assembly sequences.
The output of the first component is a set of candidate assembly sequences.
There are several candidate assembly sequences shown in (b), but the technicians manually select one of them using their experience.
In the assembly level, we check all combinations of the assembly and get a set of candidate assembly sequences.
The third element in the candidate assembly sequence of the two objects shown in Fig.2 leads to a successful plan.
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Xavier et al. [ 19] have demonstrated how optical consensus maps can be used to assess assembly accuracy when selecting from a set of candidate assemblies constructed under different assembly parameter settings.
The three candidate assemblies were evaluated by BLASTn [ 57] against Oreochromis niloticus, Oryzias latipes and Gasterosteus aculeatus cDNA dataset downloaded from Ensembl database [ 58] with an e-value threshold of 10-9.
Another candidate NPC assembly factor is Pom33p, isolated in a genetic screen for genes that are essential in cells lacking Nup133p (Chadrin et al. 2010).
Twelve candidate BAC assemblies were generated with varying parameters and the optimal assembly was identified by PCR, restriction digests, and subclone sequencing.
We generated multiple candidate BAC assemblies with varying parameters to account for potential gene collapse or artificial duplication/expansion, and experimentally validated the assemblies to identify the optimal sequence.
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