journal article Open Access Jan 01, 2018

FishTEDB: a collective database of transposable elements identified in the complete genomes of fish

View at Publisher Save 10.1093/database/bax106
Topics

No keywords indexed for this article. Browse by subject →

References
45
[1]
Mandal "SnapShot: vertebrate transposons" Cell (2008)
[2]
Finnegan "Eukaryotic transposable elements and genome evolution" Trends Genet (1989)
[3]
Wicker "A unified classification system for eukaryotic transposable elements" Nat. Rev. Genet (2007)
[4]
Biemont "Genetics: junk DNA as an evolutionary force" Nature (2006)
[5]
Capy (1997)
[6]
Finnegan "Transposable elements" Curr. Opin. Genet. Dev (1992)
[7]
Bennetzen "Transposable element contributions to plant gene and genome evolution" Plant Mol. Biol (2000)
[8]
Bennetzen "Transposable elements, gene creation and genome rearrangement in flowering plants" Curr. Opin. Genet. Dev (2005)
[9]
Bucher "Epigenetic control of transposon transcription and mobility in Arabidopsis" Cur. Opin. Plant Biol (2012)
[10]
Feschotte "Transposable elements and the evolution of regulatory networks" Nat. Rev. Genet (2008)
[11]
Long "The origin of new genes: glimpses from the young and old" Nat. Rev. Genet (2003)
[12]
Van't Hof "The industrial melanism mutation in British peppered moths is a transposable element" Nature (2016)
[13]
Ong-Abdullah "Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm" Nature (2015)
[14]
Howe "The zebrafish reference genome sequence and its relationship to the human genome" Nature (2013)
[15]
Kettleborough "A systematic genome-wide analysis of zebrafish protein-coding gene function" Nature (2013)
[16]
Amemiya "The African coelacanth genome provides insights into tetrapod evolution" Nature (2013)
[17]
Biscotti "The lungfish transcriptome: a glimpse into molecular evolution events at the transition from water to land" Sci. Rep (2016)
[18]
Capriglione "Characterization of a Tc1-like transposon in the Antarctic ice-fish, Chionodraco hamatus" Gene (2002)
[19]
Chalopin "Comparative analysis of transposable elements highlights mobilome diversity and evolution in vertebrates" Genome Biol. Evol (2015)
[20]
Gao "The contribution of transposable elements to size variations between four teleost genomes" Mob. DNA (2016)
[21]
Schemberger "Sequence analyses and chromosomal distribution of the Tc1/Mariner element in Parodontidae fish (Teleostei: Characiformes)" Gene (2016)
[22]
Jurka "Repbase Update, a database of eukaryotic repetitive elements" Cytogenet. Genome Res (2005)
[23]
Bairoch "The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999" Nucleic Acids Res (1999)
[24]
Bao "Automated de novo identification of repeat sequence families in sequenced genomes" Genome Res (2002)
[25]
Price "De novo identification of repeat families in large genomes" Bioinformatics (2005)
[26]
Lowe "tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence" Nucleic Acids Res (1997)
[27]
Nawrocki "Rfam 12.0: updates to the RNA families database" Nucleic Acids Res (2015)
[28]
McCarthy "LTR_STRUC: a novel search and identification program for LTR retrotransposons" Bioinformatics (2003)
[29]
Rho "MGEScan-non-LTR: computational identification and classification of autonomous non-LTR retrotransposons in eukaryotic genomes" Nucleic Acids Res (2009)
[30]
Kennedy "An automated homology-based approach for identifying transposable elements" BMC Bioinformatics (2011)
[31]
Abrusan "TEclass – a tool for automated classification of unknown eukaryotic transposable elements" Bioinformatics (2009)
[32]
Huang "CD-HIT Suite: a web server for clustering and comparing biological sequences" Bioinformatics (2010)
[33]
Gao "Characterization and functional annotation of nested transposable elements in eukaryotic genomes" Genomics (2012)
[34]
SanMiguel "Nested retrotransposons in the intergenic regions of the maize genome" Science (1996)
[35]
Wei "New insights into nested long terminal repeat retrotransposons in Brassica species" Mol. Plant (2013)
[36]
Altschul "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs" Nucleic Acids Res (1997)
[37]
Rice "EMBOSS: the European Molecular Biology Open Software Suite" Trends Genet (2000)
[38]
Finn "HMMER web server: interactive sequence similarity searching" Nucleic Acids Res (2011)
[39]
Finn "The Pfam protein families database: towards a more sustainable future" Nucleic Acids Res (2016)
[40]
McClintock "Controlling elements and the gene" Harb. Symp. Quant. Biol (1956)
[41]
Chuong "Regulatory activities of transposable elements: from conflicts to benefits" Nat. Rev. Genet (2017)
[42]
Clarke (2002)
[43]
Shu "Head and backbone of the early Cambrian vertebrate Haikouichthys" Nature (2003)
[44]
Volff "Genome evolution and biodiversity in teleost fish" Heredity (2005)
[45]
Bohne "Zisupton—a novel superfamily of DNA transposable elements recently active in fish" Mol. Biol. Evol (2012)
Metrics
48
Citations
45
References
Details
Published
Jan 01, 2018
Vol/Issue
2018
License
View
Funding
National Natural Science Foundation of China Award: 31272283
Michigan State University
Cite This Article
Feng Shao, Jianrong Wang, Hongen Xu, et al. (2018). FishTEDB: a collective database of transposable elements identified in the complete genomes of fish. Database, 2018. https://doi.org/10.1093/database/bax106
Related

You May Also Like