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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(3):6144-56doi: 10.3390/ijms14036144.
Yonemoto, H., Asai, K., & Hamada, M. (2013). CentroidAlign-Web: A Fast and Accurate Multiple Aligner for Long Non-Coding RNAs. International journal of molecular sciences, 14(3), 6144-56. https://doi.org/10.3390/ijms14036144
Yonemoto, Haruka, et al. "CentroidAlign-Web: A Fast and Accurate Multiple Aligner for Long Non-Coding RNAs." International journal of molecular sciences vol. 14,3 (2013): 6144-56. doi: https://doi.org/10.3390/ijms14036144
Yonemoto H, Asai K, Hamada M. CentroidAlign-Web: A Fast and Accurate Multiple Aligner for Long Non-Coding RNAs. Int J Mol Sci. 2013 Mar 18;14(3):6144-56. doi: 10.3390/ijms14036144. PMID: 23507751; PMCID: PMC3634467.
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Int J Mol Sci. 2013 Mar 18;14(3):6144-56. doi: 10.3390/ijms14036144.

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

International journal of molecular sciences

Haruka Yonemoto, Kiyoshi Asai, Michiaki Hamada

Affiliations

  1. Department of Computational Biology, Graduate School of Frontier Sciences,the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8561, Japan. [email protected].

PMID: 23507751 PMCID: PMC3634467 DOI: 10.3390/ijms14036144

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/.

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