Abstract
In this paper we present RADAR, a web-based toolkit for RNA data analysis and research. The toolkit is capable of performing database search, multiple structure alignment, and pairwise structure comparison. In addition, RADAR provides two salient features: (1) constrained alignment of RNA secondary structures, and (2) prediction of the consensus for a set of RNA secondary structures. RADAR assists scientists in performing many important RNA mining operations, including understanding the functionality of RNA sequences, the detection of structural RNA motifs and the clustering of RNA molecules, among others. The toolkit is fully operational and accessible on the Web at http://datalab.njit.edu/biodata/rna/RSmatch/server.htm