  Analyzing the properties of duplicate genes during evolution is useful to
understand the development of new cell functions. The yeast S. cerevisiae is a
useful testing ground for this problem, because its duplicated genes with
different evolutionary birth and destiny are well distinguishable. In
particular, there is a clear detection for the occurrence of a Whole Genome
Duplication (WGD) event in S. cerevisiae, and the genes derived from this event
(WGD paralogs) are known. We studied WGD and non-WGD duplicates by two parallel
analysis based on structural protein domains and on Gene Ontology annotation
scheme respectively. The results show that while a large number of
``duplicable'' structural domains is shared in local and global duplications,
WGD and non-WGD paralogs tend to have different functions. The reason for this
is the existence of WGD and non-WGD specific domains with largely different
functions. In agreement with the recent findings of Wapinski and collaborators
(Nature 449, 2007), WGD paralogs often perform ``core'' cell functions, such as
translation and DNA replication, while local duplications associate with
``peripheral'' functions such as response to stress. Our results also support
the fact that domain architectures are a reliable tool to detect homology, as
the domains of duplicates are largely invariant with date and nature of the
duplication, while their sequences and also their functions might migrate.
