RNAMotif, an RNA secondary structure definition and search algorithm

Thomas J. Macke, David J. Ecker, Robin R. Gutell, Daniel Gautheret, David A. Case, Rangarajan Sampath

Research output: Contribution to journalArticlepeer-review

386 Scopus citations


RNA molecules fold into characteristic secondary and tertiary structures that account for their diverse functional activities. Many of these RNA structures are assembled from a collection of RNA structural motifs. These basic building blocks are used repeatedly, and in various combinations, to form different RNA types and define their unique structural and functional properties. Identification of recurring RNA structural motifs will therefore enhance our understanding of RNA structure and help associate elements of RNA structure with functional and regulatory elements. Our goal was to develop a computer program that can describe an RNA structural element of any complexity and then search any nucleotide sequence database, including the complete prokaryotic and eukaryotic genomes, for these structural elements. Here we describe in detail a new computational motif search algorithm, RNAMotif, and demonstrate its utility with some motif search examples. RNAMotif differs from other motif search tools in two important aspects: first, the structure definition language is more flexible and can specify any type of base-base interaction; second, RNAMotif provides a user controlled scoring section that can be used to add capabilities that patterns alone cannot provide.

Original languageEnglish (US)
Pages (from-to)4724-4735
Number of pages12
JournalNucleic acids research
Issue number22
StatePublished - Nov 15 2001
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Genetics


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