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GenColors-based comparative genome databases for small eukaryotic genomes
Many sequence data repositories can give a quick and easily accessible overview on genomes and their annotations. Less widespread is the possibility to compare related genomes with each other in a common database environment. We have previously described the GenColors database system (http://gencolo...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531143/ https://www.ncbi.nlm.nih.gov/pubmed/23193285 http://dx.doi.org/10.1093/nar/gks1176 |
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author | Felder, Marius Romualdi, Alessandro Petzold, Andreas Platzer, Matthias Sühnel, Jürgen Glöckner, Gernot |
author_facet | Felder, Marius Romualdi, Alessandro Petzold, Andreas Platzer, Matthias Sühnel, Jürgen Glöckner, Gernot |
author_sort | Felder, Marius |
collection | PubMed |
description | Many sequence data repositories can give a quick and easily accessible overview on genomes and their annotations. Less widespread is the possibility to compare related genomes with each other in a common database environment. We have previously described the GenColors database system (http://gencolors.fli-leibniz.de) and its applications to a number of bacterial genomes such as Borrelia, Legionella, Leptospira and Treponema. This system has an emphasis on genome comparison. It combines data from related genomes and provides the user with an extensive set of visualization and analysis tools. Eukaryote genomes are normally larger than prokaryote genomes and thus pose additional challenges for such a system. We have, therefore, adapted GenColors to also handle larger datasets of small eukaryotic genomes and to display eukaryotic gene structures. Further recent developments include whole genome views, genome list options and, for bacterial genome browsers, the display of horizontal gene transfer predictions. Two new GenColors-based databases for two fungal species (http://fgb.fli-leibniz.de) and for four social amoebas (http://sacgb.fli-leibniz.de) were set up. Both new resources open up a single entry point for related genomes for the amoebozoa and fungal research communities and other interested users. Comparative genomics approaches are greatly facilitated by these resources. |
format | Online Article Text |
id | pubmed-3531143 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-35311432013-03-07 GenColors-based comparative genome databases for small eukaryotic genomes Felder, Marius Romualdi, Alessandro Petzold, Andreas Platzer, Matthias Sühnel, Jürgen Glöckner, Gernot Nucleic Acids Res Articles Many sequence data repositories can give a quick and easily accessible overview on genomes and their annotations. Less widespread is the possibility to compare related genomes with each other in a common database environment. We have previously described the GenColors database system (http://gencolors.fli-leibniz.de) and its applications to a number of bacterial genomes such as Borrelia, Legionella, Leptospira and Treponema. This system has an emphasis on genome comparison. It combines data from related genomes and provides the user with an extensive set of visualization and analysis tools. Eukaryote genomes are normally larger than prokaryote genomes and thus pose additional challenges for such a system. We have, therefore, adapted GenColors to also handle larger datasets of small eukaryotic genomes and to display eukaryotic gene structures. Further recent developments include whole genome views, genome list options and, for bacterial genome browsers, the display of horizontal gene transfer predictions. Two new GenColors-based databases for two fungal species (http://fgb.fli-leibniz.de) and for four social amoebas (http://sacgb.fli-leibniz.de) were set up. Both new resources open up a single entry point for related genomes for the amoebozoa and fungal research communities and other interested users. Comparative genomics approaches are greatly facilitated by these resources. Oxford University Press 2013-01 2012-11-27 /pmc/articles/PMC3531143/ /pubmed/23193285 http://dx.doi.org/10.1093/nar/gks1176 Text en © The Author(s) 2012. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com. |
spellingShingle | Articles Felder, Marius Romualdi, Alessandro Petzold, Andreas Platzer, Matthias Sühnel, Jürgen Glöckner, Gernot GenColors-based comparative genome databases for small eukaryotic genomes |
title | GenColors-based comparative genome databases for small eukaryotic genomes |
title_full | GenColors-based comparative genome databases for small eukaryotic genomes |
title_fullStr | GenColors-based comparative genome databases for small eukaryotic genomes |
title_full_unstemmed | GenColors-based comparative genome databases for small eukaryotic genomes |
title_short | GenColors-based comparative genome databases for small eukaryotic genomes |
title_sort | gencolors-based comparative genome databases for small eukaryotic genomes |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531143/ https://www.ncbi.nlm.nih.gov/pubmed/23193285 http://dx.doi.org/10.1093/nar/gks1176 |
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