For a quality control of polymorphism data used for classification, we conformed that one of the nucleotides in each pair of SNP alleles was the same nucleotide at the corresponding position in the cDNA sequence.
We searched for sites within 20 bp of the heteroplasmic base substitution site that were the same nucleotide as the mutant base; likewise, we also searched for nearby sites that were the same nucleotide as the progenitor (wild type) site.
Note that the two edges of an SSR of exactly X repeated units cannot be the same nucleotide as the SSR itself.
Note that the half time of substitutions of each nucleotide is the same as for other sequences under such mutational pressure, but the rate of appearing of new nucleotides is different and the composition of the sequence would change non-linearly during evolution.
Though the gap is one nucleotide longer, the distance between the 3′-end of the gap and the 5′-end bound by the 8 kDa domain is the same as in the one-nucleotide gap structure.
Two polymorphisms in the promoter region of the IL-10 gene, −1082G/A and −592C/A [note that this is the same as the −627A/C single-nucleotide polymorphism (SNP) studied by Hsieh et al. (2003)], have been investigated in Japanese women but do not appear to influence endometriosis susceptibility in this population (Kitawaki et al., 2002).
They found that whereas the ratio of non-synonymous to synonymous nucleotide substitutions is the same between the chimpanzee and humans, this ratio is different from other primates, and greater than 1.
The term b k, b k +1 is the neighborhood nucleotides that represent A, C, G, and T. E b k, b k + 1 is the stacking energy indicating the interaction of two adjacent nucleotides, which is the same as the stacking energy used in the PDNN model.
A, C and G were mismatched with the same nucleotide; U was mismatched with C (Wu et al. 2011).
The consensus sequence for LRE is GATNC-CGATN, where N can be any nucleotide but the same nucleotide is used in both repeats.
