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dbRIP


NAR Molecular Biology Database Collection entry number 886
Song L.1, Wang J.1, Liang P.1, Grover D.2, Batzer M.A.2
1Department of Cancer Genetics, Roswell Park Cancer Institute, Elm & Carlton Streets, Buffalo, NY 4263, USA
2Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA

Database Description

dbRIP is a highly integrated database of Retrotransposon Insertion Polymorphism (RIPs) in human. It currently contains a non-redundant list of 1608 polymorphic Alus and 387 polymorphic L1s. In dbRIP, we deploy the utilities and genome annotation data of the genome browser developed at University of California at Santa Cruse for user-friend querying and integrative browsing of RIPs alongside with all other genome annotation information. Users can query RIPs by RIP IDs, genetic IDs, chromosome locations, DNA or protein sequences, ethnic group, allele frequency, gene context, disease, or author name. For each RIP, users have access to the detailed information including sequence data, classification, primers, allele frequency, unbiased heterozygosity frequency, known associated diseases, and related publications (for example, http://dbRIP.brocku.cacgi-bin/hgc?hgsid=453&o=24674119&t=24674387&g=polyAluL1&i=Yd8&c=chr1&l=0&r=66290940&db=hg17 ). The entire RIP data set is available for downloading. dbRIP is available by web access at http://dbRIP.brocku.ca. We welcome all comments and/or suggestions for improvement. You can contribute to this database by submitting your new retrotransposon insertion polymorphism data to us.

Future Developments
We plan to expand dbRIP to include other minor types of RIPs, such as SVA. We will contact the UCSC Bioinformatics group to seek the possibility of either adding new a track for the retrotransposon insertion polymorphism data or modifying the existing “Repeating Element” track in their human genome browser. We will also make the RIP data available for depositing into other related central databases.

Acknowledgements

This research is in part supported by a Roswell Park Cancer Institute (RPCI) development fund (P.L.), by National Institutes of Health grants, CA101515 (P.L.), CA16056 (RPCI), and GM59290 (M.A.B.), National Science Foundation grants, BCS-0218338 (M.A.B.) and EPS-0346411 (M.A.B.), and by the Louisiana Board of Regents Millennium Trust Health Excellence Fund HEF (2000-05)-01 (M.A.B.), and the State of Louisiana Board of Regents Support Fund (M.A.B.).


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