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This article is part of the supplement: Proceedings of the Eighth Annual MCBIOS Conference. Computational Biology and Bioinformatics for a New Decade

Open Access Proceedings

RefNetBuilder: a platform for construction of integrated reference gene regulatory networks from expressed sequence tags

Ying Li1, Ping Gong2*, Edward J Perkins3, Chaoyang Zhang1 and Nan Wang1*

Author Affiliations

1 School of Computing, University of Southern Mississippi, Hattiesburg, MS 39406, USA

2 Environmental Services, SpecPro Inc., San Antonio, TX 78216, USA

3 Environmental Laboratory, U.S. Army Engineer Research and Development Center, Vicksburg, MS 39180, USA

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BMC Bioinformatics 2011, 12(Suppl 10):S20  doi:10.1186/1471-2105-12-S10-S20

Published: 18 October 2011

Abstract

Background

Gene Regulatory Networks (GRNs) provide integrated views of gene interactions that control biological processes. Many public databases contain biological interactions extracted from experimentally validated literature reports, but most furnish only information for a few genetic model organisms. In order to provide a bioinformatic tool for researchers who work with non-model organisms, we developed RefNetBuilder, a new platform that allows construction of putative reference pathways or GRNs from expressed sequence tags (ESTs).

Results

RefNetBuilder was designed to have the flexibility to extract and archive pathway or GRN information from public databases such as the Kyoto Encyclopedia of Genes and Genomes (KEGG). It features sequence alignment tools such as BLAST to allow mapping ESTs to pathways and GRNs in model organisms. A scoring algorithm was incorporated to rank and select the best match for each query EST. We validated RefNetBuilder using DNA sequences of Caenorhabditis elegans, a model organism having manually curated KEGG pathways. Using the earthworm Eisenia fetida as an example, we demonstrated the functionalities and features of RefNetBuilder.

Conclusions

The RefNetBuilder provides a standalone application for building reference GRNs for non-model organisms on a number of operating system platforms with standard desktop computer hardware. As a new bioinformatic tool aimed for constructing putative GRNs for non-model organisms that have only ESTs available, RefNetBuilder is especially useful to explore pathway- or network-related information in these organisms.