Locomotif: from graphical motif description to RNA motif search

Motivated by the recent rise of interest in small regulatory RNAs, we present Locomotif – a new approach for locating RNA motifs that goes beyond the previous ones in three ways: (1) motif search is based on efficient dynamic programming algorithms, incorporating the established thermodynamic model of RNA secondary structure formation, (2) motifs are described graphically, using a Java-based editor, and search algorithms are derived from the graphics in a fully automatic way.