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The assembly was further refined using "Single-to-End" and "End-to-End" merging by stepwise decreasing of assembly stringency of Sulston score cutoff values (down to 1× 1×-1×).
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The results are shown in Additional file 8 and Additional file 9. Gradual decrease of assembly scores with increased repeat sequence content was observed, which supports the common understanding that repeat-rich regions of genomes are more challenging to assemble.
Decreasing kf results in an overall diminution of assembly growth, leading to a predominance of the backward (assembly-exit) reactions governed by kb.
To quantify the assembly properties of Cp149ox and define the basis of the decreased level of assembly, we determined the thermodynamics of Cp149ox assembly under equilibrium conditions.
However, because the mutant yChd1 proteins are not fully active for nucleosome assembly, it was difficult to attribute the absence of periodic nucleosome arrays in the MNase assay to decreased efficiency of assembly or to a defect in the formation of periodic nucleosome arrays.
However, such approaches are not as effective and result in decreased quality of assemblies when the two multiplicity distributions of erroneous and error-free k-mers are not separable using a simple threshold.
Short reads also decrease the power of assembly for building accurate contigs because repetitive regions create ambiguities (Treangen and Salzberg 2012).
All INC-sequences were analyzed for sequence similarity in relation to possible duplicated regions in the mitochondrial genome by using NCBI Blast [ 54], tRNAscan [ 55] and a series of decreasing assembly parameters in Sequencher [ 53].
Similar NaCl-dependent bundling was also observed for Mcas MamK, except that the efficiency of assembly decreased slightly with increasing salt concentrations from 20 200 mmol/L.
The increased numbers of ORF fragments is a result of decreased assembly quality, as indicated by the negative correlation of both the number of fragments and the percentage of the total number of predicted ORFs composed of partial sequences with N50.
Under conditions favorable for αB crystallin-tubulin mixed complexes, the pool of tubulin subunits decreased and assembly of microtubules was inhibited.
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