This article is part of the supplement: Third Annual MCBIOS Conference. Bioinformatics: A Calculated Discovery .

Proceedings

EGenBio: A Data Management System for Evolutionary Genomics and Biodiversity

Laila A Nahum^1,2 , Matthew T Reynolds¹ , Zhengyuan O Wang¹ , Jeremiah J Faith³ , Rahul Jonna⁴ , Zhi J Jiang¹ , Thomas J Meyer¹ and David D Pollock^1,5

¹  Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, LA 70803 USA

²  Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA

³  Bioinformatics Program, Boston University, Boston, MA 02215, USA

⁴  Division of Developmental Disabilities, Arizona State Department, Phoenix, AZ 85012 USA

⁵  Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA

author email corresponding author email

BMC Bioinformatics 2006, 7(Suppl 2):S7doi:10.1186/1471-2105-7-S2-S7

Published:	26 September 2006

Abstract

Background

Evolutionary genomics requires management and filtering of large numbers of diverse genomic sequences for accurate analysis and inference on evolutionary processes of genomic and functional change. We developed Evolutionary Genomics and Biodiversity (EGenBio; http://egenbio.lsu.edu webcite) to begin to address this.

Description

EGenBio is a system for manipulation and filtering of large numbers of sequences, integrating curated sequence alignments and phylogenetic trees, managing evolutionary analyses, and visualizing their output. EGenBio is organized into three conceptual divisions, Evolution, Genomics, and Biodiversity. The Genomics division includes tools for selecting pre-aligned sequences from different genes and species, and for modifying and filtering these alignments for further analysis. Species searches are handled through queries that can be modified based on a tree-based navigation system and saved. The Biodiversity division contains tools for analyzing individual sequences or sequence alignments, whereas the Evolution division contains tools involving phylogenetic trees. Alignments are annotated with analytical results and modification history using our PRAED format. A miscellaneous Tools section and Help framework are also available. EGenBio was developed around our comparative genomic research and a prototype database of mtDNA genomes. It utilizes MySQL-relational databases and dynamic page generation, and calls numerous custom programs.

Conclusion

EGenBio was designed to serve as a platform for tools and resources to ease combined analysis in evolution, genomics, and biodiversity.