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

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...

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Detalles Bibliográficos
Autores principales: Yonemoto, Haruka, Asai, Kiyoshi, Hamada, Michiaki
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Molecular Diversity Preservation International (MDPI) 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3634467/
https://www.ncbi.nlm.nih.gov/pubmed/23507751
http://dx.doi.org/10.3390/ijms14036144
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author Yonemoto, Haruka
Asai, Kiyoshi
Hamada, Michiaki
author_facet Yonemoto, Haruka
Asai, Kiyoshi
Hamada, Michiaki
author_sort Yonemoto, Haruka
collection PubMed
description 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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spelling pubmed-36344672013-05-02 CentroidAlign-Web: A Fast and Accurate Multiple Aligner for Long Non-Coding RNAs Yonemoto, Haruka Asai, Kiyoshi Hamada, Michiaki Int J Mol Sci Letter 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/. Molecular Diversity Preservation International (MDPI) 2013-03-18 /pmc/articles/PMC3634467/ /pubmed/23507751 http://dx.doi.org/10.3390/ijms14036144 Text en © 2013 by the authors; licensee MDPI, Basel, Switzerland. http://creativecommons.org/licenses/by/3.0 This article is an open-access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/).
spellingShingle Letter
Yonemoto, Haruka
Asai, Kiyoshi
Hamada, Michiaki
CentroidAlign-Web: A Fast and Accurate Multiple Aligner for Long Non-Coding RNAs
title CentroidAlign-Web: A Fast and Accurate Multiple Aligner for Long Non-Coding RNAs
title_full CentroidAlign-Web: A Fast and Accurate Multiple Aligner for Long Non-Coding RNAs
title_fullStr CentroidAlign-Web: A Fast and Accurate Multiple Aligner for Long Non-Coding RNAs
title_full_unstemmed CentroidAlign-Web: A Fast and Accurate Multiple Aligner for Long Non-Coding RNAs
title_short CentroidAlign-Web: A Fast and Accurate Multiple Aligner for Long Non-Coding RNAs
title_sort centroidalign-web: a fast and accurate multiple aligner for long non-coding rnas
topic Letter
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3634467/
https://www.ncbi.nlm.nih.gov/pubmed/23507751
http://dx.doi.org/10.3390/ijms14036144
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