Locomotif: from graphical motif description to RNA motif search

Reeder J, Reeder J, Giegerich R (2007)
Bioinformatics 23(13): I392-I400.

Konferenzbeitrag | Veröffentlicht | Englisch
 
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Autor/in
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Abstract / Bemerkung
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.
Erscheinungsjahr
2007
Band
23
Ausgabe
13
Seite(n)
I392-I400
ISSN
1367-4803
Page URI
https://pub.uni-bielefeld.de/record/1593132

Zitieren

Reeder J, Reeder J, Giegerich R. Locomotif: from graphical motif description to RNA motif search. Bioinformatics. 2007;23(13):I392-I400.
Reeder, J., Reeder, J., & Giegerich, R. (2007). Locomotif: from graphical motif description to RNA motif search. Bioinformatics, 23(13), I392-I400. doi:10.1093/bioinformatics/btm179
Reeder, J., Reeder, J., and Giegerich, R. (2007). Locomotif: from graphical motif description to RNA motif search. Bioinformatics 23, I392-I400.
Reeder, J., Reeder, J., & Giegerich, R., 2007. Locomotif: from graphical motif description to RNA motif search. Bioinformatics, 23(13), p I392-I400.
J. Reeder, J. Reeder, and R. Giegerich, “Locomotif: from graphical motif description to RNA motif search”, Bioinformatics, vol. 23, 2007, pp. I392-I400.
Reeder, J., Reeder, J., Giegerich, R.: Locomotif: from graphical motif description to RNA motif search. Bioinformatics. 23, I392-I400 (2007).
Reeder, Janina, Reeder, Jens, and Giegerich, Robert. “Locomotif: from graphical motif description to RNA motif search”. Bioinformatics 23.13 (2007): I392-I400.

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PMID: 17646322
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