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VisualRepbase: an interface for the study of occurrences of transposable element families
- Source :
- BMC Bioinformatics, Vol 9, Iss 1, p 345 (2008), BMC Bioinformatics
- Publication Year :
- 2008
- Publisher :
- BMC, 2008.
-
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.
- Subjects :
- Transposable element
Java
Interface (Java)
0206 medical engineering
02 engineering and technology
Computational biology
Biology
lcsh:Computer applications to medicine. Medical informatics
Genome
Biochemistry
03 medical and health sciences
User-Computer Interface
Chromosome (genetic algorithm)
Structural Biology
Databases, Genetic
Computer Graphics
Repeated sequence
Molecular Biology
lcsh:QH301-705.5
030304 developmental biology
computer.programming_language
Repetitive Sequences, Nucleic Acid
Genetics
0303 health sciences
Applied Mathematics
FASTA format
Chromosome Mapping
Gene Annotation
Computer Science Applications
lcsh:Biology (General)
DNA Transposable Elements
lcsh:R858-859.7
computer
020602 bioinformatics
Software
Subjects
Details
- Language :
- English
- ISSN :
- 14712105
- Volume :
- 9
- Issue :
- 1
- Database :
- OpenAIRE
- Journal :
- BMC Bioinformatics
- Accession number :
- edsair.doi.dedup.....29a4c73385a44428f2fc9fbbb1c88010