Repbase


18710569	VisualRepbase: an interface for the study of occurrences of transposable element families. [PMID: 18710569] Tempel S, Jurka M, Jurka J. Abstract BACKGROUND: Repbase is a reference database of eukaryotic repetitive DNA, which includes prototypic sequences of repeats and basic information described in annotations. Repbase already has software for entering new sequence families and for comparing the user's sequence with the database of consensus sequences. RESULTS: We describe the software named VisualRepbase and the associated database, which allow for displaying and analyzing all occurrences of transposable element families present in an annotated genome. VisualRepbase is a Java-based interface which can download selected occurrences of transposable elements, show the distribution of given families on the chromosome, and present the localization of these occurrences with regard to gene annotations and other families of transposable elements in Repbase. In addition, it has several features for saving the graphical representation of occurrences, saving all sequences in FASTA format, and searching and saving all annotated genes that are surrounded by these occurrences. CONCLUSION: VisualRepbase is available as a downloadable version. It can be found at http://girinst.org/repbase/update/visual repbase.html. BMC Bioinformatics. 2008:9() \| 10 Citations (from Europe PMC, 2025-03-29)
16093699	Repbase Update, a database of eukaryotic repetitive elements. [PMID: 16093699] Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. Abstract Repbase Update is a comprehensive database of repetitive elements from diverse eukaryotic organisms. Currently, it contains over 3600 annotated sequences representing different families and subfamilies of repeats, many of which are unreported anywhere else. Each sequence is accompanied by a short description and references to the original contributors. Repbase Update includes Repbase Reports, an electronic journal publishing newly discovered transposable elements, and the Transposon Pub, a web-based browser of selected chromosomal maps of transposable elements. Sequences from Repbase Update are used to screen and annotate repetitive elements using programs such as Censor and RepeatMasker. Repbase Update is available on the worldwide web at http://www.girinst.org/Repbase_Update.html. Cytogenet Genome Res. 2005:110(1-4) \| 2115 Citations (from Europe PMC, 2025-03-29)

VisualRepbase: an interface for the study of occurrences of transposable element families. [PMID: 18710569]

Tempel S, Jurka M, Jurka J.

BACKGROUND: Repbase is a reference database of eukaryotic repetitive DNA, which includes prototypic sequences of repeats and basic information described in annotations. Repbase already has software for entering new sequence families and for comparing the user's sequence with the database of consensus sequences.
RESULTS: We describe the software named VisualRepbase and the associated database, which allow for displaying and analyzing all occurrences of transposable element families present in an annotated genome. VisualRepbase is a Java-based interface which can download selected occurrences of transposable elements, show the distribution of given families on the chromosome, and present the localization of these occurrences with regard to gene annotations and other families of transposable elements in Repbase. In addition, it has several features for saving the graphical representation of occurrences, saving all sequences in FASTA format, and searching and saving all annotated genes that are surrounded by these occurrences.
CONCLUSION: VisualRepbase is available as a downloadable version. It can be found at http://girinst.org/repbase/update/visual repbase.html.

BMC Bioinformatics. 2008:9() | 10 Citations (from Europe PMC, 2025-03-29)

Repbase Update, a database of eukaryotic repetitive elements. [PMID: 16093699]

Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J.

Abstract

Repbase Update is a comprehensive database of repetitive elements from diverse eukaryotic organisms. Currently, it contains over 3600 annotated sequences representing different families and subfamilies of repeats, many of which are unreported anywhere else. Each sequence is accompanied by a short description and references to the original contributors. Repbase Update includes Repbase Reports, an electronic journal publishing newly discovered transposable elements, and the Transposon Pub, a web-based browser of selected chromosomal maps of transposable elements. Sequences from Repbase Update are used to screen and annotate repetitive elements using programs such as Censor and RepeatMasker. Repbase Update is available on the worldwide web at http://www.girinst.org/Repbase_Update.html.

Cytogenet Genome Res. 2005:110(1-4) | 2115 Citations (from Europe PMC, 2025-03-29)

URL:	https://www.girinst.org/repbase
Full name:	A database of eukaryotic repetitive elements.
Description:	Repbase Update is a comprehensive database of repetitive elements from diverse eukaryotic organisms. Currently, it contains over 3600 annotated sequences representing different families and subfamilies of repeats, many of which are unreported anywhere else.
Year founded:	2005
Last update:	2018-12-24
Version:	23
Accessibility:	Accessible
Country/Region:	United States

Data type:	DNA
Data object:	Animal Fungi Plant
Database category:	Gene genome and annotation
Major species:	Homo sapiens
Keywords:	repetitive elements

University/Institution:	Genetic Information Research Institute
Address:	Genetic Information Research Institute, Mountain View, CA 94043, USA.
City:
Province/State:
Country/Region:	United States
Contact name (PI/Team):	Jurka J.
Contact email (PI/Helpdesk):	jurka@girinst.org

Database Commons
a catalog of worldwide biological databases

a catalog of worldwide biological databases

Database Profile

General information

Classification & Tag

Contact information

Publications

Ranking

Community reviews

Word cloud

Tags

Related Databases

Record metadata

Research & Resources

Featured

Alliance & Collaboration

Conference & Outreach

About

Database Commons a catalog of worldwide biological databases