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Locomotif: From Graphical Motif Description to RNA Motif Search

Tuesday, October 30, 2007 - 5:55pm - 6:10pm
EE/CS 3-180
Jens Reeder (Universität Bielefeld)
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 make-file.

Availability: Locomotif is available at href=http://bibiserv.techfak.uni-bielefeld.de/locomotif>http://bibiserv.techfak.uni-bielefeld.de/locomotif.