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

By Jochen Blom, Stefan P. Albaum, Daniel Doppmeier, Alfred Pühler, Frank-Jörg Vorhölter, Martha Zakrzewski, Alexander Goesmann. BMC Bioinformatics, 2009

404 citations recorded by the source corpus.

BackgroundThe 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.ResultsTo 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.ConclusionEDGAR 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, where the precomputed data sets can be browsed.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/05fe0a7f3cd400d3c2b65ccdf2bac7cb6bb8aebc

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Citations in the corpus

OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species (2015, background): “A database named EDGAR provides Venn diagrams of the common gene pools for the comparative analysis of prokaryotic genomes (17).”
EDGAR 2.0: an enhanced software platform for comparative gene content analyses (2016, positive): “(11) which was described in the use case in (7).”
Detecting Sequence Homology at the Gene Cluster Level with MultiGeneBlast (2013, background): “2009), EDGAR (Blom et al. 2009), and Absynte (Despalins et al.”