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GyDB specifications


Unique identifier OMICS_09449
Name GyDB
Alternative name Gypsy Database
Restrictions to use None
Version 2.0
Maintained Yes

Publications for Gypsy Database

GyDB citations


The Gastrodia elata genome provides insights into plant adaptation to heterotrophy

Nat Commun
PMCID: 5915607
PMID: 29691383
DOI: 10.1038/s41467-018-03423-5

[…] and only elements contained PBS were retained; then protein domains (pol, gag and env) in candidate LTR retrotransposons were identified by searching against HMM profiles collected by Gypsy Databas (GyDB). Elements contained gag domain, protease domain, reverse transcriptase (RT) domain and integrase domain, which were considered as intact. Second, families of these intact LTR retrotransposons we […]


Structure and Distribution of Centromeric Retrotransposons at Diploid and Allotetraploid Coffea Centromeric and Pericentromeric Regions

Front Plant Sci
PMCID: 5818461
PMID: 29497436
DOI: 10.3389/fpls.2018.00175

[…] ney et al., ) with a minimum length of 150 residues as in Guyot et al. (). For each coffee genome, RT domains from Gypsy LTR-RTs were aligned using MUSCLE (Edgar, ) with RT reference domains from the Gypsy Database. Aligned sequences were used to construct a bootstrapped neighbor joining phylogenetic tree (1,000 bootstrap) with ClustalW (Thompson et al., ), edited using FigTree ( […]


Genome structure of Rosa multiflora, a wild ancestor of cultivated roses

PMCID: 5909451
PMID: 29045613
DOI: 10.1093/dnares/dsx042

[…] an E-value cutoff of 1.0. Genes related to transposable elements (TEs) were inferred according to the results of BLAST searches against the NCBI NR database, and domain searches against InterPro and GyDB 2.0 using hmmsearch in HMMER 3.0 with an E-value cutoff of 1.0. Transfer RNA genes (tRNAs) were predicted by tRNAscan-SE 1.23. Ribosomal RNA genes (rRNAs) were predicted by HMMER 3.0 searches aga […]


Isoform Sequencing Provides a More Comprehensive View of the Panax ginseng Transcriptome

PMCID: 5615361
PMID: 28914759
DOI: 10.3390/genes8090228

[…] genomic sequences of Panax notoginseng [] by searching for known TEs coding sequences against Repbase [] using TBLASTX with a cutoff 10−10. The TE sequences searched were annotated with reference of Gydb []. SSRs (simple sequence repeats) were searched using SSR finder []. […]


Evidence based gene models for structural and functional annotations of the oil palm genome

Biol Direct
PMCID: 5591544
PMID: 28886750
DOI: 10.1186/s13062-017-0191-4

[…] the RefSeq plant protein sequences. ORFs with BLASTX support were clustered using BLASTClust and CD-HIT-EST [], and subsequently filtered using the TIGR plant repeat database [], GIRI Repbase [], and Gypsy Database [] to remove ORFs similar to retroelements. The resulting set of ORFs was used as the training set to develop HMMs for three modellers, GlimmerHMM [, ], AUGUSTUS [] and SNAP [] programs […]


Filamentous ascomycete genomes provide insights into Copia retrotransposon diversity in fungi

BMC Genomics
PMCID: 5445492
PMID: 28545447
DOI: 10.1186/s12864-017-3795-2

[…] complementary approaches: sequences covering the RT/RNaseH domains were included into phylogenic analyses whereas the remaining sequences were classified using similarity searches using BLAST on the Gypsy Database, which includes clearly annotated and classified reference elements that represent all the different clades LTR-retrotransposons. In the latter case, an element was assigned to the GalE […]


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GyDB institution(s)
Biotech Vana, Valencia; Institut Cavanilles de Biodiversitat i Biología Evolutiva Universitat de València, Spain; HIV Monitoring Foundation, Amsterdam, Netherlands; CIBER de Epidemiología y Salud Pública (CIBERESP), Spain

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