  The analysis and interpretation of relationships between biological molecules
is done with the help of networks. Networks are used ubiquitously throughout
biology to represent the relationships between genes and gene products. Network
models have facilitated a shift from the study of evolutionary conservation
between individual gene and gene products towards the study of conservation at
the level of pathways and complexes. Recent work has revealed much about
chemical reactions inside hundreds of organisms as well as universal
characteristics of metabolic networks, which shed light on the evolution of the
networks. However, characteristics of individual metabolites have been
neglected in this network. The current paper provides an overview of
bioinformatics software used in visualization of biological networks using
proteomic data, their main functions and limitations of the software.
