The Gypsy Database (GyDB) of mobile genetic elements

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 termina...

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Main Authors:	Lloréns, C., Futami, R., Bezemer, D., Moya, A.
Format:	Online
Language:	English
Published:	Oxford University Press 2008
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238898/

id	pubmed-2238898
recordtype	oai_dc
spelling	pubmed-22388982008-02-12 The Gypsy Database (GyDB) of mobile genetic elements Lloréns, C. Futami, R. Bezemer, D. Moya, A. Articles 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. Oxford University Press 2008-01 2007-09-25 /pmc/articles/PMC2238898/ /pubmed/17895280 http://dx.doi.org/10.1093/nar/gkm697 Text en © 2007 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Lloréns, C. Futami, R. Bezemer, D. Moya, A.
spellingShingle	Lloréns, C. Futami, R. Bezemer, D. Moya, A. The Gypsy Database (GyDB) of mobile genetic elements
author_facet	Lloréns, C. Futami, R. Bezemer, D. Moya, A.
author_sort	Lloréns, C.
title	The Gypsy Database (GyDB) of mobile genetic elements
title_short	The Gypsy Database (GyDB) of mobile genetic elements
title_full	The Gypsy Database (GyDB) of mobile genetic elements
title_fullStr	The Gypsy Database (GyDB) of mobile genetic elements
title_full_unstemmed	The Gypsy Database (GyDB) of mobile genetic elements
title_sort	gypsy database (gydb) of mobile genetic elements
description	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.
publisher	Oxford University Press
publishDate	2008
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238898/
_version_	1611438792635318272

The Gypsy Database (GyDB) of mobile genetic elements

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