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In the permutation model, the sum of occurrence probabilities of a gene over all lists equals the gene vertex degree (see below) and thus the sum of all matrix elements is the number of edges.
This is because each edge is linked to either side of the bipartite graph with certainty and therefore the sum of occurrence probabilities over all lists (which can be calculated as the row sum if genes are listed vertically or as the column sum if genes are listed horizontally) followed by summing the results over all genes must be 1 for every edge.
We may then define the consensus sequence of these subsequences as follows: (1) C o n s e n s u s i = β i | β i / S i > 0. 6 ′ N ′ | ∀ β i / S i ≤ 0. 6 where i represents the position in the consensus sequence corresponding to the column position in PWM; β∈ {A, T, C, G}; β i is the number of occurrences of β at position i; and S i is the sum of occurrence of letters at position i.
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The sum of occurrences exceeds 304 because many papers investigated several outcomes.
CG TOT represents the percentage of cytosine and guanine, (A+T+C+G) TOT represents the sum of occurrences of A, T, C and G, and (C+G) TOT represents the sum of occurrences of C and G.
CG TOT represents the percentage of cytosine and guanine of the entire promoter, (A + T + C + G) TOT represents the sum of occurrences of A, T, C and G, and (C + G) TOT represents the sum of occurrences of C and G.
The expression (A + T + C + G) TOT represents the sum of occurrences of A, T, C and G from the sliding window sequence.
For each remaining read along with its occurrence, we calculated the relative distance to the nearest TSS and for each TSS tallied the sum of read occurrence from its upstream 2000 bp to downstream 2000 bp.
Our algorithm is mainly based on a recursive formula for rapidly computing the sum of the occurrence probabilities of all binary n-tuples with weight m whose 1s are placed among the k right-most positions.
The number of occurrences of each node are given by the sum of the occurrences of its children.
We strongly suggest that HM chief inspector of prisons records and publishes the number of occurrences of violence of different levels and a weighted sum of all occurrences with explicit weights.
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