Domain Tree-Based Analysis of Protein Architecture Evolution

Domain tree-based analysis of protein architecture evolution.

Understanding the dynamics behind domain architecture evolution is of great importance to unravel the functions of proteins. Complex architectures have been created throughout evolution by rearrangement and duplication events. An interesting question is how many times a particular architecture has been created, a form of convergent evolution or domain architecture reinvention. Previous studies ...

Tree Based Differential Evolution

In recent years a new evolutionary algorithm for optimization in continuos spaces called Differential Evolution (DE) has developed. DE turns out to need only few evaluation steps to minimize a function. This makes it an interesting candidate for problem domains with high computational costs as for instance in the automatic generation of programs. In this paper a DE-based tree discovering algori...

Evolution of protein domain architectures.

This chapter reviews the current research on how protein domain architectures evolve. We begin by summarizing work on the phylogenetic distribution of proteins, as this directly impacts which domain architectures can be formed in different species. Studies relating domain family size to occurrence have shown that they generally follow power law distributions, both within genomes and larger evol...

Tree-based Wireless Mesh Network Architecture: Topology Analysis

Wireless Mesh Networks (WMNs) represent an effective solution to the “last mile” connectivity issue. However, to satisfy users’ requirements in terms of quality of service, a clear understanding of the capabilities of WMNs is necessary. As we believe that traffic streams will mainly be oriented towards/from the network gateway therefore forming a tree-based architecture, we provide analytical e...

ONLINE SUPPLEMENTARY MATERIAL: The evolution of protein architecture and the rooting of the universal tree