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The Gypsy Database (GyDB) of mobile genetic elements.
Nucleic Acids Res. 2008 Jan; 36(Database issue):D38-46.NA

Abstract

In this article, we introduce the Gypsy Database (GyDB) of mobile genetic elements, an in-progress database devoted to the non-redundant analysis and evolutionary-based classification of mobile genetic elements. In this first version, we contemplate eukaryotic Ty3/Gypsy and Retroviridae long terminal repeats (LTR) retroelements. Phylogenetic analyses based on the gag-pro-pol internal region commonly presented by these two groups strongly support a certain number of previously described Ty3/Gypsy lineages originally reported from reverse-transcriptase (RT) analyses. Vertebrate retroviruses (Retroviridae) are also constituted in several monophyletic groups consistent with genera proposed by the ICTV nomenclature, as well as with the current tendency to classify both endogenous and exogenous retroviruses by three major classes (I, II and III). Our inference indicates that all protein domains codified by the gag-pro-pol internal region of these two groups agree in a collective presentation of a particular evolutionary history, which may be used as a main criterion to differentiate their molecular diversity in a comprehensive collection of phylogenies and non-redundant molecular profiles useful in the identification of new Ty3/Gypsy and Retroviridae species. The GyDB project is available at http://gydb.uv.es.

Authors+Show Affiliations

Biotech Vana, Valencia, Institut Cavanilles de Biodiversitat i Biología Evolutiva Universitat de València, Spain.No affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

17895280

Citation

Lloréns, C, et al. "The Gypsy Database (GyDB) of Mobile Genetic Elements." Nucleic Acids Research, vol. 36, no. Database issue, 2008, pp. D38-46.
Lloréns C, Futami R, Bezemer D, et al. The Gypsy Database (GyDB) of mobile genetic elements. Nucleic Acids Res. 2008;36(Database issue):D38-46.
Lloréns, C., Futami, R., Bezemer, D., & Moya, A. (2008). The Gypsy Database (GyDB) of mobile genetic elements. Nucleic Acids Research, 36(Database issue), D38-46.
Lloréns C, et al. The Gypsy Database (GyDB) of Mobile Genetic Elements. Nucleic Acids Res. 2008;36(Database issue):D38-46. PubMed PMID: 17895280.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - The Gypsy Database (GyDB) of mobile genetic elements. AU - Lloréns,C, AU - Futami,R, AU - Bezemer,D, AU - Moya,A, Y1 - 2007/09/25/ PY - 2007/9/27/pubmed PY - 2008/3/18/medline PY - 2007/9/27/entrez SP - D38 EP - 46 JF - Nucleic acids research JO - Nucleic Acids Res VL - 36 IS - Database issue N2 - In this article, we introduce the Gypsy Database (GyDB) of mobile genetic elements, an in-progress database devoted to the non-redundant analysis and evolutionary-based classification of mobile genetic elements. In this first version, we contemplate eukaryotic Ty3/Gypsy and Retroviridae long terminal repeats (LTR) retroelements. Phylogenetic analyses based on the gag-pro-pol internal region commonly presented by these two groups strongly support a certain number of previously described Ty3/Gypsy lineages originally reported from reverse-transcriptase (RT) analyses. Vertebrate retroviruses (Retroviridae) are also constituted in several monophyletic groups consistent with genera proposed by the ICTV nomenclature, as well as with the current tendency to classify both endogenous and exogenous retroviruses by three major classes (I, II and III). Our inference indicates that all protein domains codified by the gag-pro-pol internal region of these two groups agree in a collective presentation of a particular evolutionary history, which may be used as a main criterion to differentiate their molecular diversity in a comprehensive collection of phylogenies and non-redundant molecular profiles useful in the identification of new Ty3/Gypsy and Retroviridae species. The GyDB project is available at http://gydb.uv.es. SN - 1362-4962 UR - https://www.unboundmedicine.com/medline/citation/17895280/The_Gypsy_Database__GyDB__of_mobile_genetic_elements_ L2 - https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkm697 DB - PRIME DP - Unbound Medicine ER -