Abstract
BackgroundRepbase 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.ResultsWe 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.ConclusionVisualRepbase is available as a downloadable version. It can be found at .
Highlights
Repbase is a reference database of eukaryotic repetitive DNA, which includes prototypic sequences of repeats and basic information described in annotations
As far as we know, there are only four databases of Transposable elements (TEs) which are not specialized in a single family or genome: Repbase [5], MIPS Repeat Element Database [6], the Plant Repeat Database Project of TIGR [7] and TREP database [8]
The last table stores updates of the interface and data
Summary
Database We have created six tables named: Exons, Introns, Genes, NonCodingZones, Transposons and Updates. Visual results of the search The second section of VisualRepbase is designed for a different type of search It is composed of a graphical window, a table of the occurrences, and a text field displaying the sequence of the selected item. The third section displays chromosomes with a graphical representation of TEs and other annotated features, tables of occurrences, and sequence information This figure illustrates an example of two TE families from Repbase (AtREP1; AtREP3) on chromosome 2 of Arabidopsis thaliana. This shows that the L4 family is more divergent than the CHARLIE1 family, and it indicates that it is older [17]
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
