The Gypsy Database (GyDB) of mobile genetic elements: release 2.0
This article introduces the second release of the Gypsy Database of Mobile Genetic Elements (GyDB 2.0): a research project devoted to the evolutionary dynamics of viruses and transposable elements based on their phylogenetic classification (per lineage and protein domain). The Gypsy Database (GyDB)...
| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | article |
| Language: | Inglés |
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2017
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| Online Access: | http://hdl.handle.net/20.500.11939/5505 |
| _version_ | 1855032289368473600 |
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| author | Llorens, Carlos Futami, Ricardo Covelli, Laura Dominguez-Escriba, Laura Viu, Jose M. Tamarit, Daniel Aguilar-Rodriguez, Jose Vicente-Ripolles, Miguel Fuster, Gonzalo Bernet, Guillermo P. Maumus, Florian Munoz-Pomer, Alfonso Sempere, Jose M. Latorre, Amparo Moya, Andres |
| author_browse | Aguilar-Rodriguez, Jose Bernet, Guillermo P. Covelli, Laura Dominguez-Escriba, Laura Fuster, Gonzalo Futami, Ricardo Latorre, Amparo Llorens, Carlos Maumus, Florian Moya, Andres Munoz-Pomer, Alfonso Sempere, Jose M. Tamarit, Daniel Vicente-Ripolles, Miguel Viu, Jose M. |
| author_facet | Llorens, Carlos Futami, Ricardo Covelli, Laura Dominguez-Escriba, Laura Viu, Jose M. Tamarit, Daniel Aguilar-Rodriguez, Jose Vicente-Ripolles, Miguel Fuster, Gonzalo Bernet, Guillermo P. Maumus, Florian Munoz-Pomer, Alfonso Sempere, Jose M. Latorre, Amparo Moya, Andres |
| author_sort | Llorens, Carlos |
| collection | ReDivia |
| description | This article introduces the second release of the Gypsy Database of Mobile Genetic Elements (GyDB 2.0): a research project devoted to the evolutionary dynamics of viruses and transposable elements based on their phylogenetic classification (per lineage and protein domain). The Gypsy Database (GyDB) is a long-term project that is continuously progressing, and that owing to the high molecular diversity of mobile elements requires to be completed in several stages. GyDB 2.0 has been powered with a wiki to allow other researchers participate in the project. The current database stage and scope are long terminal repeats (LTR) retroelements and relatives. GyDB 2.0 is an update based on the analysis of Ty3/Gypsy, Retroviridae, Ty1/Copia and Bel/Pao LTR retroelements and the Caulimoviridae pararetroviruses of plants. Among other features, in terms of the aforementioned topics, this update adds: (i) a variety of descriptions and reviews distributed in multiple web pages; (ii) protein-based phylogenies, where phylogenetic levels are assigned to distinct classified elements; (iii) a collection of multiple alignments, lineage-specific hidden Markov models and consensus sequences, called GyDB collection; (iv) updated RefSeq databases and BLAST and HMM servers to facilitate sequence characterization of new LTR retroelement and caulimovirus queries; and (v) a bibliographic server. GyDB 2.0 is available at http://gydb.org. |
| format | article |
| id | ReDivia5505 |
| institution | Instituto Valenciano de Investigaciones Agrarias (IVIA) |
| language | Inglés |
| publishDate | 2017 |
| publishDateRange | 2017 |
| publishDateSort | 2017 |
| record_format | dspace |
| spelling | ReDivia55052025-04-25T14:43:08Z The Gypsy Database (GyDB) of mobile genetic elements: release 2.0 Llorens, Carlos Futami, Ricardo Covelli, Laura Dominguez-Escriba, Laura Viu, Jose M. Tamarit, Daniel Aguilar-Rodriguez, Jose Vicente-Ripolles, Miguel Fuster, Gonzalo Bernet, Guillermo P. Maumus, Florian Munoz-Pomer, Alfonso Sempere, Jose M. Latorre, Amparo Moya, Andres This article introduces the second release of the Gypsy Database of Mobile Genetic Elements (GyDB 2.0): a research project devoted to the evolutionary dynamics of viruses and transposable elements based on their phylogenetic classification (per lineage and protein domain). The Gypsy Database (GyDB) is a long-term project that is continuously progressing, and that owing to the high molecular diversity of mobile elements requires to be completed in several stages. GyDB 2.0 has been powered with a wiki to allow other researchers participate in the project. The current database stage and scope are long terminal repeats (LTR) retroelements and relatives. GyDB 2.0 is an update based on the analysis of Ty3/Gypsy, Retroviridae, Ty1/Copia and Bel/Pao LTR retroelements and the Caulimoviridae pararetroviruses of plants. Among other features, in terms of the aforementioned topics, this update adds: (i) a variety of descriptions and reviews distributed in multiple web pages; (ii) protein-based phylogenies, where phylogenetic levels are assigned to distinct classified elements; (iii) a collection of multiple alignments, lineage-specific hidden Markov models and consensus sequences, called GyDB collection; (iv) updated RefSeq databases and BLAST and HMM servers to facilitate sequence characterization of new LTR retroelement and caulimovirus queries; and (v) a bibliographic server. GyDB 2.0 is available at http://gydb.org. 2017-06-01T10:12:28Z 2017-06-01T10:12:28Z 2011 JAN 2011 article publishedVersion Llorens, C., Futami, R., Covelli, L., Dominguez-Escriba, L., Viu, J.M., Tamarit, D. et al. (2011). The Gypsy Database (GyDB), of mobile genetic elements: release 2.0. Nucleic acids research, 39, D70-D74. 0305-1048 http://hdl.handle.net/20.500.11939/5505 10.1093/nar/gkq1061 en openAccess Impreso |
| spellingShingle | Llorens, Carlos Futami, Ricardo Covelli, Laura Dominguez-Escriba, Laura Viu, Jose M. Tamarit, Daniel Aguilar-Rodriguez, Jose Vicente-Ripolles, Miguel Fuster, Gonzalo Bernet, Guillermo P. Maumus, Florian Munoz-Pomer, Alfonso Sempere, Jose M. Latorre, Amparo Moya, Andres The Gypsy Database (GyDB) of mobile genetic elements: release 2.0 |
| title | The Gypsy Database (GyDB) of mobile genetic elements: release 2.0 |
| title_full | The Gypsy Database (GyDB) of mobile genetic elements: release 2.0 |
| title_fullStr | The Gypsy Database (GyDB) of mobile genetic elements: release 2.0 |
| title_full_unstemmed | The Gypsy Database (GyDB) of mobile genetic elements: release 2.0 |
| title_short | The Gypsy Database (GyDB) of mobile genetic elements: release 2.0 |
| title_sort | gypsy database gydb of mobile genetic elements release 2 0 |
| url | http://hdl.handle.net/20.500.11939/5505 |
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