Skip Navigation

Bioinformatics 2007 23(13):i392-i400; doi:10.1093/bioinformatics/btm179
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Google Scholar
Right arrow Articles by Reeder, J.
Right arrow Articles by Giegerich, R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Reeder, J.
Right arrow Articles by Giegerich, R.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Locomotif: from graphical motif description to RNA motif search

Janina Reeder , Jens Reeder and Robert Giegerich *

Faculty of Technology, Bielefeld University, D-33615 Bielefeld, Germany

*To whom correspondence should be addressed.


  Abstract

Motivation and 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.

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

Contact: robert{at}techfak.uni-bielefeld.de


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
C. Theis, J. Reeder, and R. Giegerich
KnotInFrame: prediction of -1 ribosomal frameshift events
Nucleic Acids Res., October 1, 2008; 36(18): 6013 - 6020.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.