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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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Formato: | Texto |
Lenguaje: | English |
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Oxford University Press
2008
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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/. |
format | Text |
id | pubmed-2447718 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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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