Prioritization:Phylogenetic profiles
From silico.biotoul.fr
(Difference between revisions)
Barriot (Talk | contribs)
(Created page with '== 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 g…')
Newer edit →
(Created page with '== 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 g…')
Newer edit →
Revision as of 15:28, 20 January 2011
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.
