Toward an Integrated RNA Motif Database

  • Jason T. L. Wang
  • Dongrong Wen
  • Bruce A. Shapiro
  • Katherine G. Herbert
  • Jing Li
  • Kaushik Ghosh
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4544)


In this paper we present the design and implementation of an RNA structural motif database, called RmotifDB. The structural motifs stored in RmotifDB come from three sources: (1) collected manually from biomedical literature; (2) submitted by scientists around the world; and (3) discovered by a wide variety of motif mining methods. We present here a motif mining method in detail. We also describe the interface and search mechanisms provided by RmotifDB as well as techniques used to integrate RmotifDB with the Gene Ontology. The RmotifDB system is fully operational and accessible on the Internet at


Gene Ontology Structural Motif Eukaryotic mRNAs Iron Response Element Motif Database 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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  1. 1.
    Akmaev, V.R., Kelley, S.T., Stormo, G.D.: Phylogenetically enhanced statistical tools for RNA structure prediction. Bioinformatics 16, 501–512 (2000)CrossRefGoogle Scholar
  2. 2.
    Bakheet, T., Frevel, M., Williams, B.R., Greer, W., Khabar, K.S.: ARED: human AU-rich element-containing mRNA database reveals an unexpectedly diverse functional repertoire of encoded proteins. Nucleic Acids Res. 29, 246–254 (2001)CrossRefGoogle Scholar
  3. 3.
    Bindewald, E., Shapiro, B.A.: RNA secondary structure prediction from sequence alignments using a network of k-nearest neighbor classifiers. RNA 12, 342–352 (2006)CrossRefGoogle Scholar
  4. 4.
    Bindewald, E., Schneider, T.D., Shapiro, B.A.: CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments. Nucleic Acids Res. 34, 405–411 (2006)CrossRefGoogle Scholar
  5. 5.
    Cohen.-Boulakia, S., Davidson, S.B., Froidevaux, C.: A user-centric framework for accessing biological sources and tools. In: Proc. of the 2nd International Workshop on Data Integration in the Life Sciences, pp. 3–18 (2005)Google Scholar
  6. 6.
    Dalgaard, P.: Introductory Statistics with R. Springer, Heidelberg (2004)Google Scholar
  7. 7.
    Davidson, S.B., Crabtree, J., Brunk, B.P., Schug, J., Tannen, V., Overton, G.C., Stoeckert Jr., C.J.: K2/Kleisli and GUS: experiments in integrated access to genomic data sources. IBM Systems Journal 40, 512–531 (2001)Google Scholar
  8. 8.
    Eddy, S.R.: A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure. BMC Bioinformatics 3(18) (2002)Google Scholar
  9. 9.
    Gorodkin, J., Stricklin, S.L., Stormo, G.D.: Discovering common stem-loop motifs in unaligned RNA sequences. Nucleic Acids Res. 29, 2135–2144 (2001)CrossRefGoogle Scholar
  10. 10.
    Grillo, G., Licciulli, F., Liuni, S., Sbisa, E., Pesole, G.: PatSearch: a program for the detection of patterns and structural motifs in nucleotide sequences. Nucleic Acids Res. 31, 3608–3612 (2003)CrossRefGoogle Scholar
  11. 11.
    Hofacker, I.L.: Vienna RNA secondary structure server. Nucleic Acids Res. 31, 3429–3431 (2003)CrossRefGoogle Scholar
  12. 12.
    Jones, S.G., Moxon, S., Marshall, M., Khanna, A., Eddy, S.R., Bateman, A.: Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res. 33,D121–D124 (2005)CrossRefGoogle Scholar
  13. 13.
    Khaladkar, M., Bellofatto, V., Wang, J.T.L., Tian, B., Zhang, K.: RADAR: an interactive web-based toolkit for RNA data analysis and research. In: Proc. of the 6th IEEE Symposium on Bioinformatics and Bioengineering, pp. 209–212. IEEE Computer Society Press, Los Alamitos (2006)CrossRefGoogle Scholar
  14. 14.
    Lewis, B.P., Shih, I.H., Jones-Rhoades, M.W., Bartel, D.P., Burge, C.B.: Prediction of mammalian microRNA targets. Cell. 115, 787–798 (2003)CrossRefGoogle Scholar
  15. 15.
    Liu, J., Wang, J.T.L., Hu, J., Tian, B.: A method for aligning RNA secondary structures and its application to RNA motif detection. BMC Bioinformatics 6(89) (2005)Google Scholar
  16. 16.
    Mignone, F., Grillo, G., Licciulli, F., Iacono, M., Liuni, S., Kersey, P.J., Duarte, J., Saccone, C., Pesole, G.: UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Res. 33, 141–146 (2005)CrossRefGoogle Scholar
  17. 17.
    Pruitt, K.D., Katz, K.S., Sicotte, H., Maglott, D.R.: Introducing RefSeq and LocusLink: curated human genome resources at the NCBI. Trends Genet 16, 44–47 (2000)CrossRefGoogle Scholar
  18. 18.
    Wang, J.T.L., Rozen, S., Shapiro, B.A., Shasha, D., Wang, Z., Yin, M.: New techniques for DNA sequence classification. Journal of Computational Biology 6, 209–218 (1999)Google Scholar
  19. 19.
    Wang, J.T.L., Shapiro, B.A., Shasha, D., Zhang, K., Currey, K.M.: An algorithm for finding the largest approximately common substructures of two trees. IEEE Transactions on Pattern Analysis and Machine Intelligence 20, 889–895 (1998)CrossRefGoogle Scholar
  20. 20.
    Wang, J.T.L., Wu, X.: Kernel design for RNA classification using support vector machines. International Journal of Data Mining and Bioinformatics 1, 57–76 (2006)CrossRefGoogle Scholar

Copyright information

© Springer Berlin Heidelberg 2007

Authors and Affiliations

  • Jason T. L. Wang
    • 1
  • Dongrong Wen
    • 1
  • Bruce A. Shapiro
    • 2
  • Katherine G. Herbert
    • 3
  • Jing Li
    • 4
  • Kaushik Ghosh
    • 4
  1. 1.Bioinformatics Program and Department of Computer Science, New Jersey Institute of Technology, Newark, NJ 07102 
  2. 2.Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, MD 21702 
  3. 3.Department of Computer Science, Montclair State University, Montclair, NJ 07043 
  4. 4.Applied Statistics Program and Department of Mathematical Sciences, New Jersey Institute of Technology, Newark, NJ 07102 

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