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Nucleic Acids Research Advance Access published online on May 21, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn258
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© 2008 The Author(s)
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.

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RNALogo: a new approach to display structural RNA alignment

Tzu-Hao Chang1, Jorng-Tzong Horng1,2 and Hsien-Da Huang3,4,*

1Department of Computer Science and Information Engineering, 2Department of Life Science, National Central University, Chung-Li 320, 3Institute of Bioinformatics and 4Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 300, Taiwan

*To whom correspondence should be addressed: Tel: +886 3 5712121 56952; Fax: +886 3 5729288; Email: bryan{at}mail.nctu.edu.tw

Received February 19, 2008. Revised April 7, 2008. Accepted April 20, 2008.

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/.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors


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