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This image model y(x) is composed of a number of instances of the pattern field, each representing a local PSF, in this case, located at a position x i and scaled by a factor a i corresponding to the strength of the ideal point source.
Moreover, P b[ x i(m o)] is the frequency of occurrence of the m o-gram obtained over the instances of the pattern within a background sequence.
On average, a randomly selected FFL instance breaks the connection between less than 1% of all connected pairs of genes, which is lower than for instances of the pattern ID = 12.
(12) S p (x n ) = ∑ i = 1 n - m o + 1 P r [ x i (m o ) ] log (P r [ x i (m o ) ] P b [ x i (m o ) ] ) where m o is the order of the Markov model built with the available background sequences and P r[ x i(m o)] is the frequency of occurrence of the sequence x i, …, x i−mo + 1 obtained by averaging over the instances of the pattern.
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This function represents the log-likelihood ratio between two hypotheses: the patch centered on x corresponding to an instance of the pattern versus corresponding to the background.
The latter depends solely on the distance to the block center in relative terms; in absolute terms, it also depends on the scale factor a i of the instance of the pattern.
With it Eq. 2 also states the topological significance of a randomly chosen instance of the pattern.
The second group uses patterns with 'mismatch representation' which define a signal to be a consensus pattern and allow up to a certain number of mismatches to occur in each instance of the pattern.
For each pattern in each dynamic network we computed the mean functional enrichment score that measures the tendency of genes composing an instance of the pattern to have the same GO annotation (Methods, Figure 3).
A PERL script was used to find instances of this pattern in the genome sequence of Fol4287, downloaded from the broad website (http://www.broadinstitute.org/annotation/genome/fusarium_group/MultiHome.html).html
Below I list the most conspicuous instances of this pattern of discontinuity in the biological and pre-biological domains, and outline the central aspects of the respective evolutionary transitions.
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