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Bielefeld University Bioinformatic Service

RNAforester Online

RNAforester is a command line based tool for comparing RNA secondary structures. It supports the computation of pairwise and multiple alignment of structures based on the tree alignment model (see References). The user interface follows the philosophy of the Vienna RNA Package and RNAforester Version 1.5 is part of the Vienna RNA Package Version 1.6.

New:The online version supports now calculation of multiple structure alignments.

Users of RNAforester at RNAforester are requested to cite:

Matthias Höchsmann, Thomas Töller, Robert Giegerich, Stefan Kurtz:
Local Similarity in RNA Secondary Structures in Proceedings of the IEEE Bioinformatics Conference 2003(CSB 2003) pages 159-168

Matthias Höchsmann, Björn Voss, Robert Giegerich:
Pure Multiple RNA Secondary Structure Alignments: A Progressive Profile Approach in IEEE/ACM Transactions on Computational Biology and Bioinformatics, 1(1), 2004, pages 53-62

Matthias Höchsmann: The Tree Alignment Model: Algorithms, Implementations and Applications for the Analysis of RNA Secondary Structures, Phd Thesis