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The more generous initial cutoff allows for alignment of contacts that may pass the conservative cutoff in one complex but not others.
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Furthermore, the large read size of WGS sequencing allows for alignment to larger motif types that smaller read lengths cannot span.
This coordinate system allowed for alignment of the anatomical long-axis relative to the actuator of a servo-hydraulic testing frame (Instron® 8501, Norwood, MA, USA).
This predictive ability is most likely due to the algorithms within the dotplot that allow for alignment of sequences with a high mosaic nature, both in sequence and orientation.
The genomes should be sufficiently close in order (1) to allow for unambiguous identification of orthologous genes; (2) to retain a considerable fraction of the gene order so that orthologous intergenic regions could be identified as regions between pairs of pairwise orthologous genes; and (3) to allow for alignment of orthologous intergenic regions.
By default, RelocaTE runs BLAT with a tile size of 7 and a minimum score of 10 to allow for alignments of short reads that produce an alignment with a minimal length of 10.
Alignment is done by PROLAGAN, a variation of the original Multi-LAGAN program that allows for the alignment of two alignments (profiles) and predicting ancestral contigs using a maximum matching algorithm [ 20].
To allow for alignment ambiguity in the case of frameshift variants, 5 bp upstream and downstream of an indel were extracted and compared.
When RAD-PE contigs are assembled, the small region size allows for easy alignment of even high-error sequences, and short regions of overlap are sufficient to piece sequences together.
A dedicated alignment run prior to data taking with no DUT in the beam allows for precise alignment of the telescope planes, especially for larger ε DUT.
The micromolding of multiple layers with independent features allowed for alignment between layers.
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CEO of Professional Science Editing for Scientists @ prosciediting.com