Abstract
Novel protein domain stochastic duplication/innovation models that are independent of genome-specific features are used to interpret global trends of genome evolution.
Highlights
Protein domains can be used to study proteome evolution at a coarse scale
'Chinese restaurant processes', that explains this observation with two universal parameters, representing a minimal number of domains and the relative weight of innovation to duplication
We study a model variant where new topologies are related to occurrence in genomic data, accounting for fold specificity
Summary
Protein domains can be used to study proteome evolution at a coarse scale. They are found on genomes with notable statistical distributions. It is known that the distribution of domains with a given topology follows a power law. We focus on a further aspect: these distributions, and the number of distinct topologies, follow collective trends, or scaling laws, depending on the total number of domains only, and not on genome-specific features. At the level of the proteome, an effective scale of description is provided by protein domains [1]. Domains are the basic modular topologies of folded proteins [2]. A transcription factor or an interacting pair of proteins need the Genome Biology 2009, 10:R12 http://genomebiology.com/2009/10/1/R12
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