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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doaj-6240ddd9e3aa41039caa8d9bfcf180182020-11-24T22:02:59ZengMDPI AGInternational Journal of Molecular Sciences1422-00672013-03-011436144615610.3390/ijms14036144CentroidAlign-Web: A Fast and Accurate Multiple Aligner for Long Non-Coding RNAsMichiaki HamadaHaruka YonemotoKiyoshi AsaiDue 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/.http://www.mdpi.com/1422-0067/14/3/6144ncRNAsrRNAsmultiple sequence alignment (MSA)structural alignmentsecondary structureconsensus structuresweb server |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Michiaki Hamada Haruka Yonemoto Kiyoshi Asai |
spellingShingle |
Michiaki Hamada Haruka Yonemoto Kiyoshi Asai CentroidAlign-Web: A Fast and Accurate Multiple Aligner for Long Non-Coding RNAs International Journal of Molecular Sciences ncRNAs rRNAs multiple sequence alignment (MSA) structural alignment secondary structure consensus structures web server |
author_facet |
Michiaki Hamada Haruka Yonemoto Kiyoshi Asai |
author_sort |
Michiaki Hamada |
title |
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_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_sort |
centroidalign-web: a fast and accurate multiple aligner for long non-coding rnas |
publisher |
MDPI AG |
series |
International Journal of Molecular Sciences |
issn |
1422-0067 |
publishDate |
2013-03-01 |
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/. |
topic |
ncRNAs rRNAs multiple sequence alignment (MSA) structural alignment secondary structure consensus structures web server |
url |
http://www.mdpi.com/1422-0067/14/3/6144 |
work_keys_str_mv |
AT michiakihamada centroidalignwebafastandaccuratemultiplealignerforlongnoncodingrnas AT harukayonemoto centroidalignwebafastandaccuratemultiplealignerforlongnoncodingrnas AT kiyoshiasai centroidalignwebafastandaccuratemultiplealignerforlongnoncodingrnas |
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1725833673496854528 |