Constructing structural alignment of RNA sequences by detecting and assessing conserved stems
LSMS'07 Proceedings of the 2007 international conference on Life System Modeling and Simulation
glu-RNA: aliGn highLy strUctured ncRNAs using only sequence similarity
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
Chain-RNA: A Comparative ncRNA Search Tool Based on the Two-Dimensional Chain Algorithm
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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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@m.aist.go.jp Supplementary information: The data and the supplementary information are available at http://www.ncrna.org/papers/SCARNA/.