Examples of Use
A few examples of uses for dbRIP:
- Querying Retrotransposon Insertion Polymorphisms (RIPs):
Using SearchdbRIP, you may query RIPs by RIP IDs, RIP subfamily, gene context, ethnic group name, allele frequency, disease association, etc. Using Genome Gateway, you may query RIPs by genetic IDs (gene IDs, accessions, STS, etc), and chromosome locations; Using BLAT you may search RIP by DNA or protein sequences.
- Identifying RIPs associated with particular genes:
To do this, you identify the gene of your interest as you normally do with the UCSC browser and then check the polymorphic RIP tracks for the presence of polymorphic insertions. By clicking on the individual RIP, you can obtain detailed information for each polymorphic locus with regard to sequences (flanking, TSDs, elements), classification, primers, disease association, location in gene context, and publications describing the polymorphism (click when RIP subfamily ID is displayed by mouse over the RIP tick) (example).
- Genome-wide browsing of RIPs:
You can pick a chromosome or a particular genomic region and browse all available RIPs in this region along with other genome information provided in the UCSC genome browser.
- Verifying newly identified retrontransposon insertions:
Check to see whether a putatively new insertion represents a previously known polymorphic locus or is a novel polymorphic locus.
- Genome-wide view of all RIPs from one selected class or all classes (Genome plots).
- Downloading the entire set of RIP data.
The downloadable files include the sequences of the elements and/or flanking regions for large scale analyses, such as studying the trend of new insertions and identifying insertions specific to a particular ethnic group, etc.
For information related to UCSC Genome Browser, please visit UCSC Genome Website.