Prioritization:Phylogenetic profiles

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Proximity measure

A gene profile consists of the presence/absence of an isorthologous gene (see the Data section below) in each genome of our locally hosted complete genomes database (CGDB).

The proximity measure implemented is currently the following: a distance matrix is built, consisting of the Jaccard index for each pair of genes. The proximity of a candidate gene to a set of genes is then computed as the average of the Jaccard indices of the candidate gene to each known gene.

Jaccard index (1901) coefficient of Gower & Legendre s1 = a / (a+b+c) where a is the number of co-presence and b and c the number of mismatches (d the number of co-absence is ignored).

Data

Isorthology relationship.

Isorthology automatic inference.