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Following subtraction of blank peaks, M/WT ratios were calculated for peaks generated by the same nucleotide dispensed at similar positions.
Despite the fact that often the same amino acid residue within a public CDR3 sequence is encoded by distinct triplets, others have reported that common TCR-β chains found in the synovia of two RA patients were encoded by the same nucleotide sequence [ 21].
Twenty-nine pairs (45%) were formed by the same nucleotide, suggesting that the pair preferences observed for that nucleotide is not due to base pairing, but to other unknown causes, possibly restrictions stemming from the interactions between these positions and a trans-factor.
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To test the specificity of the current approach, the polya_svm and polyadq programs, we extracted CDSs of 17600 human genes, 19600 human intronic sequences and 3748 5'-UTR regions, and generated 8261 randomized poly (A) site regions (simple randomization by maintaining the same nucleotide frequency as in original poly(A) site sequences).
Thus, aa residues 1 9 of M2e and M1 are encoded by the same nucleotides in the same reading frame and aa 10 23 of M2e and 239 252 of M1 in a different reading frame.
A problem with 454 pyrosequencing is 'blinding' of the camera due to flashing caused by incorporation of the same nucleotide in many spots, which can occur when many similar DNA templates are sequenced (Kip et al. 2011).
NAD+ has also been shown in a recent study to modulate Na+ activation in Slo2 by binding at the same nucleotide site in RCK2 (Tamsett et al., 2009).
Allele frequency of a variant is calculated by dividing the number of variant reads by total reads in the same nucleotide position.
For each observed nucleotide in the sliding-window, we divided the corresponding frequency of that nucleotide in the motif by the background frequency of the same nucleotide in all intron sequences.
Ten random DNA sequence (RDS) datasets with 10,000 sequences 601 bp in length were generated by independent and identical distribution with the same nucleotide frequencies as the yeast genomic sequences.
After the transition point the same nucleotide is reduced by the value of its initial accumulation, and the trajectory nearly returns to its starting point.
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