Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Felder, Marius, Romualdi, Alessandro, Petzold, Andreas, Platzer, Matthias, Sühnel, Jürgen, Glöckner, Gernot
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2013
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
_version_ 1782254120317485056
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
work_keys_str_mv AT feldermarius gencolorsbasedcomparativegenomedatabasesforsmalleukaryoticgenomes
AT romualdialessandro gencolorsbasedcomparativegenomedatabasesforsmalleukaryoticgenomes
AT petzoldandreas gencolorsbasedcomparativegenomedatabasesforsmalleukaryoticgenomes
AT platzermatthias gencolorsbasedcomparativegenomedatabasesforsmalleukaryoticgenomes
AT suhneljurgen gencolorsbasedcomparativegenomedatabasesforsmalleukaryoticgenomes
AT glocknergernot gencolorsbasedcomparativegenomedatabasesforsmalleukaryoticgenomes