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RNALogo: a new approach to display structural RNA alignment

Regulatory RNAs play essential roles in many essential biological processes, ranging from gene regulation to protein synthesis. This work presents a web-based tool, RNALogo, to create a new graphical representation of the patterns in a multiple RNA sequence alignment with a consensus structure. The...

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Detalles Bibliográficos
Autores principales: Chang, Tzu-Hao, Horng, Jorng-Tzong, Huang, Hsien-Da
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447718/
https://www.ncbi.nlm.nih.gov/pubmed/18495753
http://dx.doi.org/10.1093/nar/gkn258
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author Chang, Tzu-Hao
Horng, Jorng-Tzong
Huang, Hsien-Da
author_facet Chang, Tzu-Hao
Horng, Jorng-Tzong
Huang, Hsien-Da
author_sort Chang, Tzu-Hao
collection PubMed
description Regulatory RNAs play essential roles in many essential biological processes, ranging from gene regulation to protein synthesis. This work presents a web-based tool, RNALogo, to create a new graphical representation of the patterns in a multiple RNA sequence alignment with a consensus structure. The RNALogo graph can indicate significant features within an RNA sequence alignment and its consensus RNA secondary structure. RNALogo extends Sequence logos, and specifically incorporates RNA secondary structures and mutual information of base-paired regions into the graphical representation. Each RNALogo graph is composed of stacks of letters, with one stack for each position in the consensus RNA secondary structure. RNALogo provides a convenient and high configurable logo generator. An RNALogo graph is generated for each RNA family in Rfam, and these generated logos are accumulated into a gallery of RNALogo. Users can search or browse RNALogo graphs in this gallery to receive additional perspectives of known RNA families. RNALogo is now available at: http://rnalogo.mbc.nctu.edu.tw/.
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spelling pubmed-24477182008-07-09 RNALogo: a new approach to display structural RNA alignment Chang, Tzu-Hao Horng, Jorng-Tzong Huang, Hsien-Da Nucleic Acids Res Articles Regulatory RNAs play essential roles in many essential biological processes, ranging from gene regulation to protein synthesis. This work presents a web-based tool, RNALogo, to create a new graphical representation of the patterns in a multiple RNA sequence alignment with a consensus structure. The RNALogo graph can indicate significant features within an RNA sequence alignment and its consensus RNA secondary structure. RNALogo extends Sequence logos, and specifically incorporates RNA secondary structures and mutual information of base-paired regions into the graphical representation. Each RNALogo graph is composed of stacks of letters, with one stack for each position in the consensus RNA secondary structure. RNALogo provides a convenient and high configurable logo generator. An RNALogo graph is generated for each RNA family in Rfam, and these generated logos are accumulated into a gallery of RNALogo. Users can search or browse RNALogo graphs in this gallery to receive additional perspectives of known RNA families. RNALogo is now available at: http://rnalogo.mbc.nctu.edu.tw/. Oxford University Press 2008-07-01 2008-05-21 /pmc/articles/PMC2447718/ /pubmed/18495753 http://dx.doi.org/10.1093/nar/gkn258 Text en © 2008 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Chang, Tzu-Hao
Horng, Jorng-Tzong
Huang, Hsien-Da
RNALogo: a new approach to display structural RNA alignment
title RNALogo: a new approach to display structural RNA alignment
title_full RNALogo: a new approach to display structural RNA alignment
title_fullStr RNALogo: a new approach to display structural RNA alignment
title_full_unstemmed RNALogo: a new approach to display structural RNA alignment
title_short RNALogo: a new approach to display structural RNA alignment
title_sort rnalogo: a new approach to display structural rna alignment
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447718/
https://www.ncbi.nlm.nih.gov/pubmed/18495753
http://dx.doi.org/10.1093/nar/gkn258
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