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EDGAR 2.0: an enhanced software platform for comparative gene content analyses

The rapidly increasing availability of microbial genome sequences has led to a growing demand for bioinformatics software tools that support the functional analysis based on the comparison of closely related genomes. By utilizing comparative approaches on gene level it is possible to gain insights i...

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Detalles Bibliográficos
Autores principales: Blom, Jochen, Kreis, Julian, Spänig, Sebastian, Juhre, Tobias, Bertelli, Claire, Ernst, Corinna, Goesmann, Alexander
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987874/
https://www.ncbi.nlm.nih.gov/pubmed/27098043
http://dx.doi.org/10.1093/nar/gkw255
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author Blom, Jochen
Kreis, Julian
Spänig, Sebastian
Juhre, Tobias
Bertelli, Claire
Ernst, Corinna
Goesmann, Alexander
author_facet Blom, Jochen
Kreis, Julian
Spänig, Sebastian
Juhre, Tobias
Bertelli, Claire
Ernst, Corinna
Goesmann, Alexander
author_sort Blom, Jochen
collection PubMed
description The rapidly increasing availability of microbial genome sequences has led to a growing demand for bioinformatics software tools that support the functional analysis based on the comparison of closely related genomes. By utilizing comparative approaches on gene level it is possible to gain insights into the core genes which represent the set of shared features for a set of organisms under study. Vice versa singleton genes can be identified to elucidate the specific properties of an individual genome. Since initial publication, the EDGAR platform has become one of the most established software tools in the field of comparative genomics. Over the last years, the software has been continuously improved and a large number of new analysis features have been added. For the new version, EDGAR 2.0, the gene orthology estimation approach was newly designed and completely re-implemented. Among other new features, EDGAR 2.0 provides extended phylogenetic analysis features like AAI (Average Amino Acid Identity) and ANI (Average Nucleotide Identity) matrices, genome set size statistics and modernized visualizations like interactive synteny plots or Venn diagrams. Thereby, the software supports 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. All features are offered to the scientific community via a web-based and therefore platform-independent user interface, which allows easy browsing of precomputed datasets. The web server is accessible at http://edgar.computational.bio.
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spelling pubmed-49878742016-08-22 EDGAR 2.0: an enhanced software platform for comparative gene content analyses Blom, Jochen Kreis, Julian Spänig, Sebastian Juhre, Tobias Bertelli, Claire Ernst, Corinna Goesmann, Alexander Nucleic Acids Res Web Server issue The rapidly increasing availability of microbial genome sequences has led to a growing demand for bioinformatics software tools that support the functional analysis based on the comparison of closely related genomes. By utilizing comparative approaches on gene level it is possible to gain insights into the core genes which represent the set of shared features for a set of organisms under study. Vice versa singleton genes can be identified to elucidate the specific properties of an individual genome. Since initial publication, the EDGAR platform has become one of the most established software tools in the field of comparative genomics. Over the last years, the software has been continuously improved and a large number of new analysis features have been added. For the new version, EDGAR 2.0, the gene orthology estimation approach was newly designed and completely re-implemented. Among other new features, EDGAR 2.0 provides extended phylogenetic analysis features like AAI (Average Amino Acid Identity) and ANI (Average Nucleotide Identity) matrices, genome set size statistics and modernized visualizations like interactive synteny plots or Venn diagrams. Thereby, the software supports 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. All features are offered to the scientific community via a web-based and therefore platform-independent user interface, which allows easy browsing of precomputed datasets. The web server is accessible at http://edgar.computational.bio. Oxford University Press 2016-07-08 2016-04-20 /pmc/articles/PMC4987874/ /pubmed/27098043 http://dx.doi.org/10.1093/nar/gkw255 Text en © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Web Server issue
Blom, Jochen
Kreis, Julian
Spänig, Sebastian
Juhre, Tobias
Bertelli, Claire
Ernst, Corinna
Goesmann, Alexander
EDGAR 2.0: an enhanced software platform for comparative gene content analyses
title EDGAR 2.0: an enhanced software platform for comparative gene content analyses
title_full EDGAR 2.0: an enhanced software platform for comparative gene content analyses
title_fullStr EDGAR 2.0: an enhanced software platform for comparative gene content analyses
title_full_unstemmed EDGAR 2.0: an enhanced software platform for comparative gene content analyses
title_short EDGAR 2.0: an enhanced software platform for comparative gene content analyses
title_sort edgar 2.0: an enhanced software platform for comparative gene content analyses
topic Web Server issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987874/
https://www.ncbi.nlm.nih.gov/pubmed/27098043
http://dx.doi.org/10.1093/nar/gkw255
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