RNALogo: a new approach to display structural RNA alignment

Tzu-Hao Chang, Jorng-Tzong Horng, Hsien-Da Huang

Research output: Contribution to journalArticlepeer-review

34 Scopus citations


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 languageEnglish
Pages (from-to)W91-W96
Number of pages6
JournalNucleic Acids Research
StatePublished - Jul 2008



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