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/.
authors.affiliation: Department of Computer Science and Information Engineering, National Central University, Chung-Li 320, Taiwan.
authors.forename: Tzu-Hao
authors.initials: TH
authors.lastname: Chang
authors.forename: Jorng-Tzong
authors.initials: JT
authors.lastname: Horng
authors.forename: Hsien-Da
authors.initials: HD
authors.lastname: Huang
mesh_terms: D003196:Computer Graphics; D020407:Internet; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D038621:Regulatory Sequences, Ribonucleic Acid; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D038621:Regulatory Sequences, Ribonucleic Acid; D012313:RNA