PMID- 17895280
OWN - NLM
STAT- MEDLINE
DCOM- 20080317
LR  - 20240322
IS  - 1362-4962 (Electronic)
IS  - 0305-1048 (Print)
IS  - 0305-1048 (Linking)
VI  - 36
IP  - Database issue
DP  - 2008 Jan
TI  - The Gypsy Database (GyDB) of mobile genetic elements.
PG  - D38-46
AB  - 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.
FAU - Llorens, C
AU  - Llorens C
AD  - Biotech Vana, Valencia, Institut Cavanilles de Biodiversitat i Biologia Evolutiva 
      Universitat de Valencia, Spain.
FAU - Futami, R
AU  - Futami R
FAU - Bezemer, D
AU  - Bezemer D
FAU - Moya, A
AU  - Moya A
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20070925
PL  - England
TA  - Nucleic Acids Res
JT  - Nucleic acids research
JID - 0411011
RN  - 0 (Retroelements)
RN  - 0 (Retroviridae Proteins)
SB  - IM
MH  - *Databases, Genetic
MH  - Genes, Viral
MH  - Internet
MH  - Phylogeny
MH  - *Retroelements
MH  - Retroviridae/*genetics
MH  - Retroviridae Proteins/chemistry/classification/genetics
MH  - Sequence Alignment
MH  - Terminal Repeat Sequences
MH  - User-Computer Interface
PMC - PMC2238898
EDAT- 2007/09/27 09:00
MHDA- 2008/03/18 09:00
PMCR- 2007/09/25
CRDT- 2007/09/27 09:00
PHST- 2007/09/27 09:00 [pubmed]
PHST- 2008/03/18 09:00 [medline]
PHST- 2007/09/27 09:00 [entrez]
PHST- 2007/09/25 00:00 [pmc-release]
AID - gkm697 [pii]
AID - 10.1093/nar/gkm697 [doi]
PST - ppublish
SO  - Nucleic Acids Res. 2008 Jan;36(Database issue):D38-46. doi: 10.1093/nar/gkm697. 
      Epub 2007 Sep 25.