Repbase Update (www.girinst.org), is a comprehensive collection of DNA sequences, currently representing over 1200 families and subfamilies of repetitive elements from all eukaryotic species. Each family is identifiable by a unique name, referenced to published literature and often characterized in brief commentaries. Several hundreds of repetitive families added to Repbase Update during the last two years are either unreported anywhere else, or have been thoroughly revised in terms of their consensus sequences and biological classification. Our approach is based on computer-assisted exploration and analysis of publicly available DNA sequence data. Repbase Update has been routinely used by public institutions and private companies throughout the world in routine gene discovery, sequence assembly and probe design. In addition, Repbase Update became a unique resource for individual research projects of biological and medical importance. In light of the anticipated flood of new sequence data, we propose continuation of development, maintenance and electronic dissemination of this resource. In particular, we expect to discover and characterize hundreds of new repetitive families which will continue to be published electronically in Repbase Update. Furthermore, we will continue to compile and organize reported families of repeats from all eukaryotic species. Finally, we will maintain the public server for automatic annotation of human and rodent repeats and generate up-to-date annotation of repetitive elements present in genomic DNA of mammals. In particular we propose to: 1. Continue development, maintenance and electronic distribution of reference collections of repetitive elements from all sequenced eukaryotic species. 2. Generate public domain maps of repetitive elements present in available mammalian genomic DNA sequences.

Agency
National Institute of Health (NIH)
Institute
National Library of Medicine (NLM)
Type
Biotechnology Resource Grants (P41)
Project #
5P41LM006252-05
Application #
6402801
Study Section
Biomedical Library and Informatics Review Committee (BLR)
Program Officer
Florance, Valerie
Project Start
1996-09-30
Project End
2003-03-31
Budget Start
2001-05-01
Budget End
2002-04-30
Support Year
5
Fiscal Year
2001
Total Cost
$318,168
Indirect Cost
Name
Genetic Information Research Institute
Department
Type
DUNS #
City
Mountain View
State
CA
Country
United States
Zip Code
94043
Hubley, Robert; Finn, Robert D; Clements, Jody et al. (2016) The Dfam database of repetitive DNA families. Nucleic Acids Res 44:D81-9
Kojima, Kenji K (2015) A New Class of SINEs with snRNA Gene-Derived Heads. Genome Biol Evol 7:1702-12
Kojima, Kenji K; Jurka, Jerzy (2015) Ancient Origin of the U2 Small Nuclear RNA Gene-Targeting Non-LTR Retrotransposons Utopia. PLoS One 10:e0140084
Kojima, Kenji K; Jurka, Jerzy (2013) A superfamily of DNA transposons targeting multicopy small RNA genes. PLoS One 8:e68260
Wheeler, Travis J; Clements, Jody; Eddy, Sean R et al. (2013) Dfam: a database of repetitive DNA based on profile hidden Markov models. Nucleic Acids Res 41:D70-82
Jurka, Jerzy; Bao, Weidong; Kojima, Kenji K et al. (2012) Distinct groups of repetitive families preserved in mammals correspond to different periods of regulatory innovations in vertebrates. Biol Direct 7:36
Groenen, Martien A M; Archibald, Alan L; Uenishi, Hirohide et al. (2012) Analyses of pig genomes provide insight into porcine demography and evolution. Nature 491:393-8
Lehnert, Stefan; Kapitonov, Vladimir; Thilakarathne, Pushpike J et al. (2011) Modeling the asymmetric evolution of a mouse and rat-specific microRNA gene cluster intron 10 of the Sfmbt2 gene. BMC Genomics 12:257
Jurka, Jerzy; Bao, Weidong; Kojima, Kenji K (2011) Families of transposable elements, population structure and the origin of species. Biol Direct 6:44
Kojima, Kenji K; Kapitonov, Vladimir V; Jurka, Jerzy (2011) Recent expansion of a new Ingi-related clade of Vingi non-LTR retrotransposons in hedgehogs. Mol Biol Evol 28:17-20

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