Title: Design of an RNA structural motif database

Authors: Dongrong Wen, Jason T.L. Wang

Addresses: Bioinformatics Program and Department of Computer Science, New Jersey Institute of Technology, Newark, NJ 07102, USA. ' Bioinformatics Program and Department of Computer Science, New Jersey Institute of Technology, Newark, NJ 07102, USA

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: collected manually from the biomedical literature; submitted by scientists around the world; 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 and report its current status. The RmotifDB system is fully operational and accessible on the web at http://datalab.njit.edu/bioinfo/.

Keywords: RNA structural motifs; untranslated regions; database design; motif mining; interface mechanisms; search; computational intelligence; bioinformatics.

DOI: 10.1504/IJCIBSB.2009.024042

International Journal of Computational Intelligence in Bioinformatics and Systems Biology, 2009 Vol.1 No.1, pp.32 - 41

Published online: 24 Mar 2009 *