RNAMotif, an RNA secondary structure definition and search algorithm

RNA molecules fold into characteristic secondary and tertiary structures th at account for their diverse functional activities. Many of these RNA struc tures 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 prope rties. Identification of recurring RNA structural motifs will therefore enh ance 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 compl exity and then search any nucleotide sequence database, including the compl ete 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 dif fers from other motif search tools in two important aspects: first, the str ucture definition language is more flexible and can specify any type of bas e-base interaction; second, RNAMotif provides a user controlled scoring sec tion that can be used to add capabilities that patterns alone cannot provid e.