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Four different attributes were calculated for each reference alignment, which reflect the overall difficulty of the alignment: the total number of sequences to be aligned, the average length of the sequences to be aligned, the norMD score which is an objective function for MSA based on the Mean Distance (MD) scores introduced in ClustalX [63].
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And clearly, the number and complexity of the variant molecules in cases of LHP may impact the difficulty of alignment and the accuracy with which the authentic template sequences are detected due to reference bias [84 86].
The main cause of difficulty lies in the alignment of oral, pharyngeal and tracheal axes to expose the glottis with Macintosh.
In addition, an intraspecies alignment tends to be less accurate than an interspecies one, due to the difficulty of computing alignment scores corresponding to the actual divergence time [ 52].
Microsporidia is not included in the phylogenetic analyses based on 18S rDNA due to highly divergence of the sequences and difficulty in the alignment.
That highlights the difficulty of continuous alignment of two different systems.
Furthermore, the tolerance of misalignment existing in inter-ONUs traffic is investigated and analyzed for all-optical encoding operation, and the difficulty of pulse alignment is proved to be lower.
To reduce difficulties with the alignment of sequences for the detection of single nucleotide polymorphisms (SNPs), often 'reduced representation libraries' are used that include only a subset of sequences from several individuals representative for different populations [ 27, 28] or from tissue-specific transcriptomes (RNAseq) [ 29].
Nakashima et al. reported three cases of osteoporotic vertebral fracture complicated by Parkinson's disease, all of which showed significant deterioration of sagittal alignment due to postoperative compression fracture or sinking of the fusion cage, suggesting the difficulty of maintaining sagittal alignment even with posteroanterior surgery [ 13].
This is partly due to difficulties in the alignment of ITS2 sequences in more distant taxa.
As αW43 constitutes a part of the β-strand 4 and there are a few highly conserved amino acid residues near this position, we did not have any difficulties with the alignment of the position 43 between teleost fish and tetrapod class II α chain sequences.
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CEO of Professional Science Editing for Scientists @ prosciediting.com