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In the first round of selection, the S t r i c t- T assembly was the best of these three assemblies because it has a cumulative size close to 200 Mb (Table 2 and Fig. 5), the estimated size of the T. castaneum genome, and a small difference between non-redundant aligned length or breadth of alignment, and total aligned length (Fig. 5, Table 3 and Additional file 4).
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These newly assembled optical contigs become the updated reference for 8 cycles of alignment and assembly, which increase their breadth and depth.
The alignment pipeline used in PolyPhen-2 selects homologous sequences using a clustering algorithm and then constructs and refines the alignment yielding an alignment containing both orthologs and paralogs that may or may not be full length, which yields a wider breadth of sequences but decreased depth compared with the curated alignments used with Align-GVGD and SIFT [ 36].
Or out of alignment".
"I'm all out of alignment".
"Well out of alignment there," he pronounces.
Lack of alignment.
Feeling out of alignment?
Where am I out of alignment?
The planets are out of alignment.
Do you see areas of alignment?
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com