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CentroidAlign-Web: A Fast and Accurate Multiple Aligner for Long Non-Coding RNAs
Department of Computational Biology, Graduate School of Frontier Sciences,the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8561, Japan
Computational Biology Research Center (CBRC), the National Institute of Advanced Industrial Science and Technology (AIST), Tokyo Waterfront Bio-IT Research Building, 2-4-7 Aomi, Koto-ku,Tokyo 135-0064, Japan
* Author to whom correspondence should be addressed.
Received: 20 November 2012; in revised form: 28 January 2013 / Accepted: 28 February 2013 / Published: 18 March 2013
Abstract: Due to the recent discovery of non-coding RNAs (ncRNAs), multiple sequence alignment (MSA) of those long RNA sequences is becoming increasingly important for classifying and determining the functional motifs in RNAs. However, not only primary (nucleotide) sequences, but also secondary structures of ncRNAs are closely related to their function and are conserved evolutionarily. Hence, information about secondary structures should be considered in the sequence alignment of ncRNAs. Yet, in general, a huge computational time is required in order to compute MSAs, taking secondary structure information into account. In this paper, we describe a fast and accurate web server, called CentroidAlign-Web, which can handle long RNA sequences. The web server also appropriately incorporates information about known secondary structures into MSAs. Computational experiments indicate that our web server is fast and accurate enough to handle long RNA sequences. CentroidAlign-Web is freely available from http://centroidalign.ncrna.org/.
Keywords: ncRNAs; rRNAs; multiple sequence alignment (MSA); structural alignment; secondary structure; consensus structures; web server
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Yonemoto, H.; Asai, K.; Hamada, M. CentroidAlign-Web: A Fast and Accurate Multiple Aligner for Long Non-Coding RNAs. Int. J. Mol. Sci. 2013, 14, 6144-6156.
Yonemoto H, Asai K, Hamada M. CentroidAlign-Web: A Fast and Accurate Multiple Aligner for Long Non-Coding RNAs. International Journal of Molecular Sciences. 2013; 14(3):6144-6156.
Yonemoto, Haruka; Asai, Kiyoshi; Hamada, Michiaki. 2013. "CentroidAlign-Web: A Fast and Accurate Multiple Aligner for Long Non-Coding RNAs." Int. J. Mol. Sci. 14, no. 3: 6144-6156.