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RSDB

http://rsdb.csie.ncu.edu.tw

J. T. Horng¹, H. D. Horng², F. M. Lin², L. W. Lu², J. H. Lin², H. C. chang², T. T. Weng⁴, C. Y. Kao³

¹Department of Life Science, National Central University, Taiwan
²Department of Computer Science and Information Engineering, National Central University, Taiwan
³Department of Computer Science and Information Engineering, National Taiwan University, Taiwan
⁴Asia Bioinnovations Corporation

Contact   damay@db.csie.ncu.edu.tw

Database Description

At least 43% of the human genome is occupied by repetitive elements. Ever more, around 51% of the rice genome is occupied by repetitive elements. The analysis of repetitive elements reveals repetitive elements in our genome may have been very important in the evolutionary genomics. The RSDB database contains repetitive elements, which are classified into exact, tandem, and similar. The length of the repetitive elements is longer than 7 bp and that in tandem repeats is 2-6 bp. The interfaces to query and show the results are also provided. Statistical data such as the relationship between repetitive elements and genes, cross-references of repetitive elements among different organisms and so on are also provided. Finally, we address three applications of the repetitive elements stored in RSDB. The complete contents of RSDB are available to the public at website: http://rsdb.csie.ncu.edu.tw. The readers may download partial query results.

Recent Developments

The work [11] estimated that at least 43% of the human genome is occupied by four major classes of interspersed repetitive elements, i.e., LINEs, SINEs, LTR elements, and DAN transposons. The analysis in this work has provided some insights into the evolutionary genomes of the human genome. There are many repetitive elements in our genome, and they may have been very important in the evolutionary genomics. RepBase and STRBase are two representative databases of repeat sequences. RepBase is a collection of repeat sequences, and its goal is to collect, review and systematically organize representative examples or consensus sequences of repetitive elements from all eukaryotic species. STRBase stores microsatellites (short tandem repeats, STRs) which contains 2-5 bp (base pairs) repeats. These repeats are widespread throughout the human genome and show sufficient variability among individuals in a population that they have become important in several fields including genetic mapping, linkage analysis, and human identity testing.

Acknowledgements

The authors would like to thank the National Science Council of the Republic of China and Asia Bioinnovation Corporation for financially supporting this research. Prof. Ueng-Cheng Yang and Dr. Yu-Chung Chang are appreciated for their valuable discussion regarding molecular biology.

REFERENCES

1. S.F. Altschul, W. Gish, W. Miller, E.W. Myers, and D.J. Lipman. (1990) Basic local alignment search tool,J. Mol. Biol., 215, 403-410.
2. D.A. Benson, M.S. Boguski, D.J. Lipman, J. Ostell, B.F. Ouellette, B.A. Rapp, and D.L. Wheeler. (1999) GenBank, Nucleic Acids Res., 27, 12-17.
3. V. Biaudet, F. Samson, and P. Bessieres. (1997) Micado--a network-oriented database for microbial genomes, Comput. Applic. Biosci., 13,431-438.
4. C. Burks, Molecular Biology Database List. (1999) Nucleic Acids Res., 27,1-9.
5. I.K. Cheang, Y.B. Choi, and A. Tang. (1994) Overview of the Structures of Heterogeneous Genome Databases, Proceedings of the 27th Hawaii International Conference on System Sciences, Biotechnology Computing, 5, 15 V24.
6. J. Courteau, (1991) Genome Databases, Science, 254, 201-207.
7. R. Elmasri and S.B. Navathe, Fundamentals of Database Systems, 2nd edn. Addison-Wesley Publishing Company, Menlo Park, CA. (1994)
8. T. Etzold, A. Ulyanov, and P. Argos, (1996) SRS: information retrieval system for molecular biology data banks, Methods Enzymol., 266,114-128.
9. C. Harger, et al. (1998) The Genome Sequence DataBase (GSDB): improving data quality and data access. Nucleic Acids Res., 26,21-26.
10. H. Kitakami, T. Shin-I, K. Ikeo, Y. Ugawa, N. Saitou, T. Gojobori, and Y. Tateno. (1995) YAMATO and ASUKA: DNA Database Management System, Proceedings of the 28th Hawaii International Conference on System Sciences, 5, 72-80.
11. Li W.H, Gu Z., Wang H., and Nekrutenko A. (2001) Evolutionary analyses of the human genome, Nature, 409,847-849.
12. R. Sargent, D. Fuhrman, T. Critchlow, T.D. Sera, R. Mecklenburg,G. Lindstrom,G., and G.D. Schuler,J.A. Epstein, H. Ohkawa, and J.A. Kans. (1996) Entrez: molecular biology database and retrieval system, Methods Enzymol., 266,141-162.
13. G. Stoesser, M.A. Moseley, J. Sleep, M. McGowran, M. Garcia-Pastor, and P. Sterk. (1998) The EMBL nucleotide sequence database, Nucleic Acids Res., 26,8-15.
14. L. Wall, T. Christiansen, R.L. Schwartz, Programming Perl, 2nd edn. O'Reilly & Associates, Sebastopol, CA. (1996)
15. J.T. Horng, J.H. Lin, and C.Y. Kao. RSDB-A Database of Repetitive Elements in Complete Genomes, Proceedings of the Atlantic Symposium on Computational Biology and Genome Information Systems & Technology, Durham, NC, USA, (2001) pp. 220-223

Category   Gene Identification and Structure