Locomotif: from graphical motif description to RNA motif search.
RESULTS
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. The editor allows us to draw secondary structures, annotated with size and sequence information. They closely resemble the established, but informal way in which RNA motifs are communicated in the literature. Thus, the learning effort for Locomotif users is minimal. (3) Locomotif employs a client-server approach. Motifs are designed by the user locally. Search programs are generated and compiled on a bioinformatics server. They are made available both for execution on the server, and for download as C source code plus an appropriate makefile.


BACKGROUND
Locomotif is available at http://bibiserv.techfak.uni-bielefeld.de/locomotif.
Reeder
Janina
J
Faculty of Technology, Bielefeld University, D-33615 Bielefeld, Germany.
Reeder
Jens
J
Giegerich
Robert
R
D000465:Algorithms; D001483:Base Sequence; D003628:Database Management Systems; D030541:Databases, Genetic; D016247:Information Storage and Retrieval / Q000379:methods*; D008969:Molecular Sequence Data; D012313:RNA / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
D012313:RNA