EDGAR: a software framework for the comparative analysis of prokaryotic genomes.
Jochen Blom,Stefan P. Albaum,Daniel Doppmeier,Alfred Pühler,Frank-Jörg Vorhölter,Martha Zakrzewski,Alexander Goesmann +6 more
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TLDR
EDGAR provides novel analysis features and significantly simplifies the comparative analysis of related genomes and supports a quick survey of evolutionary relationships and simplifying the process of obtaining new biological insights into the differential gene content of kindred genomes.Abstract:
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. 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. 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
, where the precomputed data sets can be browsed.read more
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Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42.
Xiao-Hua Chen,Alexandra Koumoutsi,Romy Scholz,Andreas Eisenreich,Kathrin Schneider,Isabelle Heinemeyer,Burkhard Morgenstern,Björn Voss,Wolfgang R. Hess,Oleg N. Reva,Helmut Junge,Birgit Voigt,Peter R. Jungblut,Joachim Vater,Roderich D. Süssmuth,Heiko Liesegang,Axel Strittmatter,Gerhard Gottschalk,Rainer Borriss +18 more
TL;DR: The B. amyloliquefaciens FZB42 genome reveals an unexpected potential to produce secondary metabolites, including the polyketides bacillaene and difficidin, and identifies four giant gene clusters absent in B. subtilis 168.
Journal ArticleDOI
OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species
TL;DR: A web platform named OrthoVenn that is useful for genome wide comparisons and visualization of orthologous clusters and allows for a customized search of clusters of specific genes through key words or BLAST is reported.
Journal ArticleDOI
Pathogenomics of Xanthomonas: understanding bacterium–plant interactions
Robert P. Ryan,Frank-Jörg Vorhölter,Neha Potnis,Jeffrey B. Jones,Marie-Anne Van Sluys,Adam J. Bogdanove,J. Maxwell Dow +6 more
TL;DR: In this Review, the insights that functional and comparative genomic studies are providing into the adaptation of this group of bacteria to exploit the extraordinary diversity of plant hosts and different host tissues are discussed.
Journal ArticleDOI
The Genome of Akkermansia muciniphila, a Dedicated Intestinal Mucin Degrader, and Its Use in Exploring Intestinal Metagenomes
Mark W. J. van Passel,Ravi Kant,Erwin G. Zoetendal,Caroline M. Plugge,Muriel Derrien,Stephanie Malfatti,Stephanie Malfatti,Patrick S. G. Chain,Patrick S. G. Chain,Tanja Woyke,Airi Palva,Willem M. de Vos,Willem M. de Vos,Hauke Smidt +13 more
TL;DR: Large repositories of GI tract metagenomes allow us to further mine for genetic heterogeneity and species diversity in the genus Akkermansia, providing novel insight towards the functionality of this abundant inhabitant of the human intestinal tract.
Journal ArticleDOI
EDGAR 2.0: an enhanced software platform for comparative gene content analyses.
Jochen Blom,Julian Kreis,Sebastian Spänig,Tobias Juhre,Claire Bertelli,Corinna Ernst,Alexander Goesmann +6 more
TL;DR: The new version of EDGAR 2.0 provides a quick and user-friendly survey of evolutionary relationships between microbial genomes and simplifies the process of obtaining new biological insights into their differential gene content.
References
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Journal ArticleDOI
Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
Journal ArticleDOI
MUSCLE: multiple sequence alignment with high accuracy and high throughput
TL;DR: MUSCLE is a new computer program for creating multiple alignments of protein sequences that includes fast distance estimation using kmer counting, progressive alignment using a new profile function the authors call the log-expectation score, and refinement using tree-dependent restricted partitioning.
Journal ArticleDOI
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David L. Wheeler,Deanna M. Church,Ron Edgar,Scott Federhen,Wolfgang Helmberg,Thomas L. Madden,Joan Pontius,Gregory D. Schuler,Lynn M. Schriml,Edwin Sequeira,Tugba O. Suzek,Tatiana Tatusova,Lukas Wagner +12 more
TL;DR: In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s website.
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