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Nucleic Acids Research Advance Access originally published online on May 21, 2007
Nucleic Acids Research 2007 35(Web Server issue):W300-W304; doi:10.1093/nar/gkm253
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Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W300-W304
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

RADAR: a web server for RNA data analysis and research

Mugdha Khaladkar1, Vivian Bellofatto2, Jason T. L. Wang1, Bin Tian3 and Bruce A. Shapiro4,*

1Bioinformatics Program and Department of Computer Science, New Jersey Institute of Technology, NJ 07102, 2Department of Microbiology and Molecular Genetics, University of Medicine and Dentistry of New Jersey-New Jersey Medical School, International Center for Public Health, 225 Warren Street, Newark, NJ 07103, 3Department of Biochemistry and Molecular Biology, University of Medicine and Dentistry of New Jersey-New Jersey Medical School, Newark, NJ 07101 and 4Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, MD 21702, USA

*To whom correspondence should be addressed. Tel: +1 301 846 5536; Fax: +1 301 846 5598; Email: bshapiro{at}ncifcrf.gov

Received January 22, 2007. Revised March 26, 2007. Accepted April 8, 2007.

RADAR is a web server that provides a multitude of functionality for RNA data analysis and research. It can align structure-annotated RNA sequences so that both sequence and structure information are taken into consideration during the alignment process. This server is capable of performing pairwise structure alignment, multiple structure alignment, database search and clustering. In addition, RADAR provides two salient features: (i) constrained alignment of RNA secondary structures, and (ii) prediction of the consensus structure for a set of RNA sequences. RADAR will be able to assist scientists in performing many important RNA mining operations, including the understanding of the functionality of RNA sequences, the detection of RNA structural motifs and the clustering of RNA molecules, among others. The web server together with a software package for download is freely accessible at http://datalab.njit.edu/biodata/rna/RSmatch/server.htm and http://www.ccrnp.ncifcrf.gov/~bshapiro/


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