A Complex Network Approach to Phylogenetic Analysis using Protein Sequence Databases

This work comprises data mining of protein sequences related to the
chitin metabolic pathway of completely sequenced genomes of extant
organisms pertaining to the three life domains, followed by
meta-analysis using traditional sequence similarity comparison and
complex network approaches. Complex
networks involving proteins of the chitin metabolic pathway in extant
organisms were constructed based on protein sequence similarity. Several
usual network indices are used to obtain information on the topology of
these networks, including those related to higher order neighborhood
properties and the concept of distance between networks. Due to the
assumed evolutionary character of the system, we also discuss issues
related to modularity properties, with the concept of edge betweenness
playing a particularly important role in our analysis. Complex network
approach correctly identifies clusters of organisms that belong to
phylogenetic groups without any a priori knowledge about the biological
features of the investigated protein sequences. We envisage the prospect
of using such a complex network approach as a high-throughput
phylogenetic method.