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One factor potentially influencing difficulty in assembly is the abundance of both simple and complex repeats.
The remaining singletons could have resulted from various reasons such as incompleteness of known databases, sequencing errors, short read lengths leading to difficulty in assembly etc. [ 8, 31].
An additional advantage of use of transcriptome data over genomic data is due to the difficulty in assembly and annotation of multigene families in genomes.
Due to the difficulty in assembly of the non-coding region, the total lengths of the maxicircles were estimated based on coverage values of the coding region, assuming relatively equal coverage throughout the entire maxicircle and a population of maxicircles of equal size.
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This problem arises due the difficulty in assemblying fast-evolving regions, such as the subtelomeres of each chromosome.
Dave Hyde of The Fort Lauderdale Sun Sentinel is a bit amused by all the premature freaking out and Gary Washburn of The Boston Globe writes that the Heat should have expected some difficulties in assembly.
In November 2012 Foxconn chairman Terry Gou reported that the delay in production was due to undisclosed difficulties in assembly.
The localization of human Lamin C, lacking a CaaX box, displays internal nuclear localization, which is similar to that observed for Drosophila Lamin C. Lamin B2 shows somewhat aberrant localization, suggesting difficulties in assembly, which nevertheless, under controlled heat shock treatment did not affect viability.
These numbers are unreliable, however, as repetitive regions usually become compressed during alignment, and sequences present in multiple locations cause difficulties in assembly of contiguous chromosomes.
The potential for biparental inheritance of the plastid genome and subsequent heteroplasmy may have further contributed to difficulties in assembly when using a single maternal family.
Despite the difficulties in assembly encountered in virulent strains, the study was not negatively impacted since genomic coverage of these strains was still substantially high (> 84%) when aligned over the T2Bo_vir reference genome.
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