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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)

Abstract

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 http://datalab.njit.edu/bioinfo/

Keywords

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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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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