This makes absolute comparisons of RNA abundance for different sequences problematic.
The variation in the number of LRR repeats makes credible sequence alignment of the full protein sequences problematic, and thus only the relatively conserved TIR domains were used in the phylogenetic analysis.
Moreover, the introduction of PCR errors using Sanger-based sequencing is problematic, particularly when sequencing from cloned DNA.
The placement of No. 3 in this sequence is problematic because he worked on it for over a decade, starting sketches for it soon after beginning work on No. 5, but completing it after both Nos. 5 and 4. The Symphony No. 1 in C minor for full-scale orchestra was written in 1824, when Mendelssohn was aged 15.
Expecting the generally divergent nature of OBPs sequences (∼20% amino acid identity over all sequences) to make the sequence alignment problematic [49], we used several multiple sequence alignment (MSA) methods to evaluate potential different outcomes of using six alignment approaches (Table 2), which differ greatly in popularity and general approach to the MSA problem [50].
Because the investigation was initiated prior to release of the assembled bovine genome, direct comparison between bovine genomic and bFLIC sequence was problematic.
Illumina TruSeq synthetic long-reads can span up to 18.5 kb; however, they fail to assemble if the sequence has problematic regions longer than the component reads used to assemble the synthetic reads (e.g. in the heterochromatin) [ 8].
Assembly of large tandem repeat DNA sequence is problematic for in silico assembly, in particular the challenge of whether to align two identical sequences as the same or separate given that in vivo they may actually be immediately adjacent to one another.
In general, longer reads are desirable, especially where mapping the location of a sequence is problematic and mutations other than base substitutions are expected, but there appears to be a trade-off between read length and factors such as cost and, arguably, accuracy.
Previous attempts to assemble the subtelomeric regions from SC5314 whole-genome sequencing were problematic specifically due to the presence of this same sequence element that we termed the Bermuda Triangle sequence (BTS).
