Software

EDGAR: A software framework for the comparative analysis of prokaryotic genomes

Jochen Blom¹ , Stefan P Albaum¹ , Daniel Doppmeier¹ , Alfred Pühler³ , Frank-Jörg Vorhölter³ , Martha Zakrzewski¹ and Alexander Goesmann^1,2

¹  Computational Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany

²  Bioinformatics Resource Facility, CeBiTec, Bielefeld University, Bielefeld, Germany

³  Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Bielefeld, Germany

author email corresponding author email

BMC Bioinformatics 2009, 10:154doi:10.1186/1471-2105-10-154

Published:	20 May 2009

Abstract

Background

The introduction of next generation sequencing approaches has caused a rapid increase in the number of completely sequenced genomes. As one result of this development, it is now feasible to analyze large groups of related genomes in a comparative approach. A main task in comparative genomics is the identification of orthologous genes in different genomes and the classification of genes as core genes or singletons.

Results

To support these studies EDGAR – "Efficient Database framework for comparative Genome Analyses using BLAST score Ratios" – was developed. EDGAR is designed to automatically perform genome comparisons in a high throughput approach. Comparative analyses for 582 genomes across 75 genus groups taken from the NCBI genomes database were conducted with the software and the results were integrated into an underlying database. To demonstrate a specific application case, we analyzed ten genomes of the bacterial genus Xanthomonas, for which phylogenetic studies were awkward due to divergent taxonomic systems. The resultant phylogeny EDGAR provided was consistent with outcomes from traditional approaches performed recently and moreover, it was possible to root each strain with unprecedented accuracy.

Conclusion

EDGAR provides novel analysis features and significantly simplifies the comparative analysis of related genomes. The software supports a quick survey of evolutionary relationships and simplifies the process of obtaining new biological insights into the differential gene content of kindred genomes. Visualization features, like synteny plots or Venn diagrams, are offered to the scientific community through a web-based and therefore platform independent user interface http://edgar.cebitec.uni-bielefeld.de webcite, where the precomputed data sets can be browsed.