The coffee genome hub: a resource for coffee genomes
The whole genome sequence of Coffea canephora, the perennial diploid species known as Robusta, has been recently released. In the context of the C. canephora genome sequencing project and to support post-genomics efforts, we developed the Coffee Genome Hub (http://coffee-genome.org/), an integrative...
| Main Authors: | , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Oxford University Press
2015
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/66031 |
| _version_ | 1855519172413358080 |
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| author | Dereeper, A. Bocs, S. Rouard, M. Guignon, Valentin Ravel, S. Tranchant-Dubreuil, C. Poncet, V. Garsmeur, O. Lashermes, P. Droc, Gaëtan |
| author_browse | Bocs, S. Dereeper, A. Droc, Gaëtan Garsmeur, O. Guignon, Valentin Lashermes, P. Poncet, V. Ravel, S. Rouard, M. Tranchant-Dubreuil, C. |
| author_facet | Dereeper, A. Bocs, S. Rouard, M. Guignon, Valentin Ravel, S. Tranchant-Dubreuil, C. Poncet, V. Garsmeur, O. Lashermes, P. Droc, Gaëtan |
| author_sort | Dereeper, A. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | The whole genome sequence of Coffea canephora, the perennial diploid species known as Robusta, has been recently released. In the context of the C. canephora genome sequencing project and to support post-genomics efforts, we developed the Coffee Genome Hub (http://coffee-genome.org/), an integrative genome information system that allows centralized access to genomics and genetics data and analysis tools to facilitate translational and applied research in coffee. We provide the complete genome sequence of C. canephora along with gene structure, gene product information, metabolism, gene families, transcriptomics, syntenic blocks, genetic markers and genetic maps. The hub relies on generic software (e.g. GMOD tools) for easy querying, visualizing and downloading research data. It includes a Genome Browser enhanced by a Community Annotation System, enabling the improvement of automatic gene annotation through an annotation editor. In addition, the hub aims at developing interoperability among other existing South Green tools managing coffee data (phylogenomics resources, SNPs) and/or supporting data analyses with the Galaxy workflow manager. |
| format | Journal Article |
| id | CGSpace66031 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2015 |
| publishDateRange | 2015 |
| publishDateSort | 2015 |
| publisher | Oxford University Press |
| publisherStr | Oxford University Press |
| record_format | dspace |
| spelling | CGSpace660312025-11-12T05:39:37Z The coffee genome hub: a resource for coffee genomes Dereeper, A. Bocs, S. Rouard, M. Guignon, Valentin Ravel, S. Tranchant-Dubreuil, C. Poncet, V. Garsmeur, O. Lashermes, P. Droc, Gaëtan coffea coffea canephora data data analysis genomes information systems genetics The whole genome sequence of Coffea canephora, the perennial diploid species known as Robusta, has been recently released. In the context of the C. canephora genome sequencing project and to support post-genomics efforts, we developed the Coffee Genome Hub (http://coffee-genome.org/), an integrative genome information system that allows centralized access to genomics and genetics data and analysis tools to facilitate translational and applied research in coffee. We provide the complete genome sequence of C. canephora along with gene structure, gene product information, metabolism, gene families, transcriptomics, syntenic blocks, genetic markers and genetic maps. The hub relies on generic software (e.g. GMOD tools) for easy querying, visualizing and downloading research data. It includes a Genome Browser enhanced by a Community Annotation System, enabling the improvement of automatic gene annotation through an annotation editor. In addition, the hub aims at developing interoperability among other existing South Green tools managing coffee data (phylogenomics resources, SNPs) and/or supporting data analyses with the Galaxy workflow manager. 2015-01-28 2015-05-13T13:59:47Z 2015-05-13T13:59:47Z Journal Article https://hdl.handle.net/10568/66031 en Open Access application/pdf Oxford University Press Dereeper, A.; Bocs, S.; Rouard, M.; Guignon, V.; Ravel, S.; Tranchant-Dubreuil, C.; Poncet, V.; Garsmeur, O.; Lashermes, P.; Droc, G. (2015) The coffee genome hub: a resource for coffee genomes. Nucleic Acids Research 43 (D1): D1028-D1035. ISSN: 0305-1048 |
| spellingShingle | coffea coffea canephora data data analysis genomes information systems genetics Dereeper, A. Bocs, S. Rouard, M. Guignon, Valentin Ravel, S. Tranchant-Dubreuil, C. Poncet, V. Garsmeur, O. Lashermes, P. Droc, Gaëtan The coffee genome hub: a resource for coffee genomes |
| title | The coffee genome hub: a resource for coffee genomes |
| title_full | The coffee genome hub: a resource for coffee genomes |
| title_fullStr | The coffee genome hub: a resource for coffee genomes |
| title_full_unstemmed | The coffee genome hub: a resource for coffee genomes |
| title_short | The coffee genome hub: a resource for coffee genomes |
| title_sort | coffee genome hub a resource for coffee genomes |
| topic | coffea coffea canephora data data analysis genomes information systems genetics |
| url | https://hdl.handle.net/10568/66031 |
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