RNALogo: a new approach to display structural RNA alignment.

Tzu Hao Chang, Jorng Tzong Horng, Hsien Da Huang

Research output: Contribution to journalArticle

32 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 languageEnglish
JournalNucleic Acids Research
Volume36
Issue numberWeb Server issue
DOIs
Publication statusPublished - Jul 1 2008
Externally publishedYes

Fingerprint

RNA
Sequence Alignment
Position-Specific Scoring Matrices
Biological Phenomena
Genes
Proteins

ASJC Scopus subject areas

  • Genetics

Cite this

RNALogo : a new approach to display structural RNA alignment. / Chang, Tzu Hao; Horng, Jorng Tzong; Huang, Hsien Da.

In: Nucleic Acids Research, Vol. 36, No. Web Server issue, 01.07.2008.

Research output: Contribution to journalArticle

Chang, Tzu Hao ; Horng, Jorng Tzong ; Huang, Hsien Da. / RNALogo : a new approach to display structural RNA alignment. In: Nucleic Acids Research. 2008 ; Vol. 36, No. Web Server issue.
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