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Open Access Software review

Open source tool for prediction of genome wide protein-protein interaction network based on ortholog information

Chandra Sekhar Pedamallu and Janos Posfai*

Author Affiliations

New England Biolabs, Ipswich, MA, USA

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Source Code for Biology and Medicine 2010, 5:8  doi:10.1186/1751-0473-5-8

Published: 4 August 2010

Abstract

Background

Protein-protein interactions are crucially important for cellular processes. Knowledge of these interactions improves the understanding of cell cycle, metabolism, signaling, transport, and secretion. Information about interactions can hint at molecular causes of diseases, and can provide clues for new therapeutic approaches. Several (usually expensive and time consuming) experimental methods can probe protein - protein interactions. Data sets, derived from such experiments make the development of prediction methods feasible, and make the creation of protein-protein interaction network predicting tools possible.

Methods

Here we report the development of a simple open source program module (OpenPPI_predictor) that can generate a putative protein-protein interaction network for target genomes. This tool uses the orthologous interactome network data from a related, experimentally studied organism.

Results

Results from our predictions can be visualized using the Cytoscape visualization software, and can be piped to downstream processing algorithms. We have employed our program to predict protein-protein interaction network for the human parasite roundworm Brugia malayi, using interactome data from the free living nematode Caenorhabditis elegans.

Availability

The OpenPPI_predictor source code is available from http://tools.neb.com/~posfai/ webcite.