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With the assistance of the expert's judgment, an arrangement of correlation matrices was built for all components in a level and then change individual correlation judgments into proportion scale estimations (Kannan et al., 2008).
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For the 3DZD, similarity matrices were built based on the three different measures of the correlation coefficient (r), DE, and DM.
Here t RB offline is the time of the Offline RB construction and storage, t RB online is the time of an Online RB computation, while t FE is the time for a FE computation, once FE matrices are built.
DALI's actual alignment process requires a similarity search after the two proteins' distance matrices are built; this is normally conducted via a series of overlapping submatrices of size 6x6.
Binding matrices were built using the standard Delila programs [19], [20].
In order to quantify the rates by which amino acids are replaced by other amino acids so-called substitution matrices (or exchange matrices) are built from multiple sequence alignments of homologous proteins [1].
Since substitution matrices are built from fully functional proteins it can be assumed that during an exchange one amino acid is preferably replaced by one with similar physico-chemical properties.
Phylogenetic analyses and distance matrices were built using the Mega5 package [ 19].
Another two IBD matrices were built up for two different genotyping structures: moderate and extensive gaps.
Migration matrices were built describing numbers of connections between 27 subtype H3N2 or 29 subtype H1N1 predefined geographic regions.
The networks for Γ f matrices were built with the same contact/noncontact filtering applied to the I LL n matrix (see preceding section).
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