Affiliations: Institute for Advanced Biosciences, Keio University,
Fujisawa, 252-8520, Japan | Bioinformatics Program, Graduate School of Media and
Governance, Keio University, Fujisawa, 252-8520, Japan | Department of Environmental Information, Keio
University, Fujisawa, 252-8520, Japan
Abstract: Analysis and visualization of biological networks, such as
protein-protein and protein-DNA interactions, are crucially important toward
obtaining a thorough understanding of living systems. Here, we present an
integrative software platform, eXpanda, which enables an analysis of a very
broad range of biological networks, with a special focus on the extraction of
characteristic topologies which potentially function as units in the networks.
eXpanda is provided as a Perl library which gives full-automatic connections to
various biological databases via a Perl programmable interface and can perform
topological analysis based on graph theory. The results of these analyses are
visualizable by vector graphics. eXpanda is under GNU General Public License.
Software package, detailed documentations, source codes, and some sample
scripts are downloadable at http://medcd.iab.keio.ac.jp/expanda/.