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SCARNA: Fast and Accurate Structural Alignment of RNA Sequences by Matching Fixed-Length Stem Fragments

MPG-Autoren
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Tabei,  Y
Department Empirical Inference, Max Planck Institute for Biological Cybernetics, Max Planck Society;

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Tsuda,  K
Department Empirical Inference, Max Planck Institute for Biological Cybernetics, Max Planck Society;

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Zitation

Tabei, Y., Tsuda, K., Kin, T., & Asai, K. (2006). SCARNA: Fast and Accurate Structural Alignment of RNA Sequences by Matching Fixed-Length Stem Fragments. Bioinformatics, 22(14), 1723-1729. doi:10.1093/bioinformatics/btl177.


Zitierlink: http://hdl.handle.net/11858/00-001M-0000-0013-D1D9-7
Zusammenfassung
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 their potential secondary structures. Sankoffamp;lsquo;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. 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 to the much slower existing algorithms.