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Int. J. Mol. Sci. 2013, 14(3), 6144-6156; doi:10.3390/ijms14036144
Letter

CentroidAlign-Web: A Fast and Accurate Multiple Aligner for Long Non-Coding RNAs

1
, 1,2
 and 1,2,*
Received: 20 November 2012; in revised form: 28 January 2013 / Accepted: 28 February 2013 / Published: 18 March 2013
(This article belongs to the Special Issue Non-Coding RNAs 2012)
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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 ncRNAs; rRNAs; multiple sequence alignment (MSA); structural alignment; secondary structure; consensus structures; web server
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

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.

AMA Style

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.

Chicago/Turabian Style

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.


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