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

BMC Bioinformatics

Proceedings

Edward J Perkins¹  Ping Gong²  Chaoyang Zhang³  Ying Li³  Nan Wang³ 

[1] Environmental Laboratory, U.S. Army Engineer Research and Development Center, 39180, Vicksburg, MS, USA;Environmental Services, SpecPro Inc., 78216, San Antonio, TX, USA;School of Computing, University of Southern Mississippi, 39406, Hattiesburg, MS, USA;

关键词: Query Sequence;    Basic Local Alignment Search Tool;    Boolean Network;    KEGG Orthology;    Probabilistic Boolean Network;   

DOI  :  10.1186/1471-2105-12-S10-S20

来源: Springer

【 摘 要 】

BackgroundGene 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).ResultsRefNetBuilder 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.ConclusionsThe 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.

【 授权许可】

Unknown   
© Li et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.