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As the order of the gene islands from the downloaded CM0113 sequence did not match that of M. truncatula and white clover, they were rearranged for the purposes of alignment.
For purposes of alignment and recognition modeling the PWMs were converted to position frequency matrices (PFMs), where the elements at each position are the probabilities of each base occurring, using: However, we noticed when comparing the PWMs from orthologous HD proteins between flies, obtained using the B1H method, and mouse, using the PBM method, that there was a difference in scaling.
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The purpose of alignment is to best determine sequence homology.
A maximum of two mismatches was permitted for the purpose of alignment.
The accuracy of alignment is very important in re-sequencing because the main purpose of alignment is to discover the variants relative to a reference genome.
The table 2 of the Pei et al. study showed the diversities of the 16S rRNA genes after masking (for the purpose of alignment) and the diversities of the masked hypervariable regions, whereas our study showed the diversities of full-length 16S rRNA genes for the purpose of HGT study.
In these regions, Tbx2 is thought to repress chamber-specific gene expression such as Nppa, Smpx, Cx40, and Slit3 allowing these areas to remain as primary myocardium for purposes of chamber alignment and to form specialist structures of ECCs, valves, septa, and conduction system components (Aanhaanen et al., 2011; Christoffels et al., 2004b; Medioni et al., 2010).
With the existence of reference alignments specifically compiled for the purpose of RNA alignment benchmarks, program parameters can be specifically optimized for RNA alignments.
Hence, the purpose of the alignment is to make the curvelet coefficients of two images comparable as much as possible.
The position of each printhead can be independently controlled for the purpose of printhead alignment, by which print quality is improved without tightening the manufacturing tolerances.
The ultimate purpose of improving alignment is to make more accurate fold recognition and structure prediction.
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