Hoberman2007

CREATED: 201002051546 LINK: url:~/Modules/Literature/Hoberman2007.pdf Orthologs appear in similar genomic context compared to paralogs, they are direct evolutionary counterparts (same gene in different species)

Using sequence identity

construct gene tree (using MSA), reconcile with species tree

BBH (assumes protein similarity reflects evolutionary distance)

COG (from triangles of BBH)

OrthoMCL

INPARANOID

Using spatial information

Using gene interaction network, Bandyopadhyay2008

Using functional annotation, Zheng et al

Graph based framework, H = (V_1 u V_2, E) where V_1 are genes from G_1 and V_2 are genes from G_2. The transitive closure of H is the family graph F.

Method of Bansal et al iteratively computes a maximal matching and increase the weight

Graph based framework, H = (V_1 u V_2, E) where V_1 are genes from G_1 and V_2 are genes from G_2. The transitive closure of H is the family graph F.

Bansal et al iteratively computes a maximal matching and increase the weights of edges between genes in a max-gap clusters of edges between genes in a max-gap cluster.