RNALogo: a new approach to display structural RNA alignment.

Tzu Hao Chang; Jorng Tzong Horng; Hsien Da Huang

doi:10.1093/nar/gkn258

RNALogo: a new approach to display structural RNA alignment.

Tzu Hao Chang, Jorng Tzong Horng, Hsien Da Huang

Research output: Contribution to journal › Article › peer-review

36 Citations (Scopus)

Abstract

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/.

Original language	English
Pages (from-to)	W91-96
Journal	Nucleic Acids Research
Volume	36
Issue number	Web Server issue
DOIs	https://doi.org/10.1093/nar/gkn258
Publication status	Published - Jul 1 2008
Externally published	Yes

ASJC Scopus subject areas

Genetics

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10.1093/nar/gkn258

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title = "RNALogo: a new approach to display structural RNA alignment.",

abstract = "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/.",

author = "Chang, {Tzu Hao} and Horng, {Jorng Tzong} and Huang, {Hsien Da}",

note = "Funding Information: The authors would like to thank the National Science Council of the Republic of China for financially supporting this research under Contract No. NSC 96-3112-E-009-002 and NSC 95-2311-B-009-004-MY3. Special thanks for financial support from the National Research Program for Genomic Medicine (NRPGM), Taiwan. This work was also partially supported by MOE ATU. Ted Knoy is appreciated for his editorial assistance. Funding to pay the Open Access publication charges for this article was provided by National Science Council of the Republic of China and MOE ATU. Copyright: This record is sourced from MEDLINE{\textregistered}/PubMed{\textregistered}, a database of the U.S. National Library of Medicine",

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N2 - 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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RNALogo: a new approach to display structural RNA alignment.

Abstract

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