Bioinformatics Advance Access originally published online on May 11, 2006
Bioinformatics 2006 22(14):1723-1729; doi:10.1093/bioinformatics/btl177
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SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments
1 Department of Computational Biology, Graduate School of Frontier Science, University of Tokyo CB04 Kiban-tou 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
2 Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST) 2-42 Aomi, Koto-ku, Tokyo, 135-0064, Japan
*To whom correspondence should be addressed.
Motivation: The functions of non-coding RNAs are strongly related to their secondary structures, but it is known that a secondary structure prediction of a single sequence is not reliable. Therefore, we have to collect similar RNA sequences with a common secondary structure for the analyses of a new non-coding RNA without knowing the exact secondary structure itself. Therefore, the sequence comparison in searching similar RNAs should consider not only their sequence similarities but also their potential secondary structures. Sankoff's algorithm predicts the common secondary structures of the sequences, but it is computationally too expensive to apply to large-scale analyses. Because we often want to compare a large number of cDNA sequences or to search similar RNAs in the whole genome sequences, much faster algorithms are required.
Results: We propose a new method of comparing RNA sequences based on the structural alignments of the fixed-length fragments of the stem candidates. The implemented software, SCARNA (Stem Candidate Aligner for RNAs), is fast enough to apply to the long sequences in the large-scale analyses. The accuracy of the alignments is better or comparable with the much slower existing algorithms.
Availability: The web server of SCARNA with graphical structural alignment viewer is available at http://www.scarna.org/
Contact: scarna{at}m.aist.go.jp
Supplementary information: The data and the supplementary information are available at http://www.ncrna.org/papers/SCARNA/.
Received on August 26, 2005; revised on April 3, 2006; accepted on May 2, 2006
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