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The frequency of each sequence word was divided by its expected frequency in each observation, see [ 34] for details.
The mathematical basis for the signature is an odds ratio – p i – calculated by dividing the frequency of a length- L oligonucleotide by its expected frequency.
The RSCU value of a codon [ 38] is its observed frequency divided by its expected frequency in the absence of usage bias (which is the average frequency of all codons for that amino acid).
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N−1 residues are mainly turn associated residues (with a frequency of 48.5% which is 2.4 times its expected frequency) and coil (34.7%, 1.8 times expected).
At spacings normally used by farmers, more than 50,000,000 acres would be required to grow a population large enough to permit every genotype to occur in its expected frequency.
Performance was evaluated over an ideal set of Bayesian simulations in which each generating condition appeared at its expected frequency.
For the C+1 residues, the frequencies are more equilibrated, still showing a considerable over-representation of turns (28.3%, 1.4 times its expected frequency).
The z-score of a tetramer, Z(N1 N2 N3 N4), depicts how much the observed frequency of the tetramer N1 N2 N3 N4, O(N1 N2 N3 N4), deviates from its expected frequency E(N1 N1 N1 N1).
(A) Percentage deviation in G + C content from its expected frequency of CpG island associated promoters that contain or do not contain a degenerate TATA-box (dTATA).
(B) Percentage deviation in G + C content from its expected frequency of promoters not associated with CpG islands that contain or do not contain a degenerate TATA-box.
The CpG bias of a sequence is defined as the ratio of the observed frequency of CpG dinucleotides divided by the expected frequency of CpG dinucleotides where the expected number of CpG dinucleotides is the product of the frequency of C and G nucleotides in a given sequence.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com