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The only incompletely assembled gene is kdrb where approximately 200 bp of the coding sequence are missing.
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VTBuilder suggested that five pairs of low-abundance Trinity transcripts assemblies were incompletely assembled by the latter (three in P. elegans and two in P. flavoviridis).
Furthermore, it has to be considered that transcripts supported by only a small number of aligned reads (≤10) may reflect incompletely assembled transcripts in the reference.
One of the major obstacles hindering studies of in vivo ribosomal biogenesis stems from the complexity of the assembly process and heterogeneity of the incompletely assembled intermediates.
In addition, p7 has been shown to be necessary for capsid assembly and envelopment because mutations in p7 result in the accumulation of incompletely assembled capsids that are unable to encapsidate viral RNA.
Upon folding, native proteins can exit the ER by the secretory pathway, whereas misfolded proteins and incompletely assembled protein complexes are generally retained by a protein quality control machinery [1].
To test the completeness of the incompletely assembled genomes, we carried out two tests.
These incompletely assembled pre-40S subunits recruit the endonuclease Nob1 and form 80S-like particles.
To remove the incompletely assembled and thus linear ligation products, DNA exonuclease treatment was carried out after the multimer assembly.
An expected limitation of reconstructed transcriptomes, as compared to whole genomes, is that reconstructed genes may be incompletely assembled.
However, the positions and orders of genes within each physical contig cannot be determined because of the incompletely assembled genome sequences.
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