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Variation inherited from the parent material would produce SPF values greater than that for a random sequence.
That's more than the expected 50% for a random sequence.
For example, for the three-choice tests in my sample (A,B,C), the correct choice repeated its predecessor only 25% of the time (versus the expected 33% for a random sequence).
This fraction represents the non-conforming exons that exceed the length predicted for a random sequence.
Hypothesis 1 is that ORFs that do not code for proteins follow expectations for a random sequence of nucleotides.
Then, the Shannon information for a random sequence composed of these letters with the aforesaid probabilities would have been −1.366 rather than −1.386 = −ln4.
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For example, a random sequence may bind a transcription factor, but that may not result in transcription.
In other words, we chose to work with 28 expression patterns for which a random sequence has low fitness.
For each centre, a random sequence of permuted blocks of variable length was generated by the Clinical Trial Centre Leipzig.
In this case, working in single precision led to differences with double precision only for one sequence (a random sequence of 6000 bases) out of the 44 we examined, and these were very small (only three bases out of the 6000 were matched with a different partner).
As DREME requires a negative dataset for more accurate predictions, we generated a random sequence set for each input dataset using a third order Markov chain model based on the transition probabilities of the sequences in the dataset.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com