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The Gypsy Database (GyDB) of mobile genetic elements: release 2.0
Carlos Llorens1, Ricardo Futami, Laura Covelli
1Biotechvana, Parc Científic, Universitat de València, Calle Catedrático José Beltrán 2, 46980 Paterna, València, Spain. carlos.llorens@uv.es
Nucleic Acids Research
|November 2, 2010
Summary
The Gypsy Database (GyDB 2.0) offers evolutionary insights into mobile genetic elements, including long terminal repeat retroelements and plant pararetroviruses. This updated resource facilitates research through enhanced phylogenetic classification and collaborative tools.
Area of Science:
- Genetics and Genomics
- Evolutionary Biology
- Bioinformatics
Background:
- Mobile genetic elements, such as viruses and transposable elements, exhibit high molecular diversity.
- Understanding their evolutionary dynamics requires comprehensive and continuously updated resources.
- Previous versions of the Gypsy Database (GyDB) have laid the groundwork for this research area.
Purpose of the Study:
- To introduce the second release of the Gypsy Database (GyDB 2.0), focusing on long terminal repeats (LTR) retroelements and related elements.
- To enhance the database with new features for phylogenetic classification and sequence characterization.
- To foster community participation through a wiki interface.
Main Methods:
- Phylogenetic classification based on lineage and protein domain analysis.
- Integration of updated RefSeq databases and bioinformatics servers (BLAST, HMM).
- Development of a wiki for collaborative research and data contribution.
Main Results:
- GyDB 2.0 provides updated analysis of Ty3/Gypsy, Retroviridae, Ty1/Copia, Bel/Pao LTR retroelements, and Caulimoviridae pararetroviruses.
- Features include detailed descriptions, protein-based phylogenies, multiple alignments, HMMs, and consensus sequences (GyDB collection).
- Enhanced sequence characterization tools and a bibliographic server are now available.
Conclusions:
- GyDB 2.0 represents a significant advancement in the study of mobile genetic elements' evolutionary dynamics.
- The database serves as a valuable, collaborative resource for researchers in genetics, evolution, and bioinformatics.
- The inclusion of community-driven updates via the wiki ensures the database's continued relevance and growth.
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