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Open Access Highly Accessed Open Badges Research article

A comprehensive comparison of comparative RNA structure prediction approaches

Paul P Gardner1* and Robert Giegerich2

Author Affiliations

1 Department of Evolutionary Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark

2 Faculty of Technology, University of Bielefeld, PO Box 10 01 31, 33501 Bielefeld, Germany

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BMC Bioinformatics 2004, 5:140  doi:10.1186/1471-2105-5-140

Published: 30 September 2004



An increasing number of researchers have released novel RNA structure analysis and prediction algorithms for comparative approaches to structure prediction. Yet, independent benchmarking of these algorithms is rarely performed as is now common practice for protein-folding, gene-finding and multiple-sequence-alignment algorithms.


Here we evaluate a number of RNA folding algorithms using reliable RNA data-sets and compare their relative performance.


We conclude that comparative data can enhance structure prediction but structure-prediction-algorithms vary widely in terms of both sensitivity and selectivity across different lengths and homologies. Furthermore, we outline some directions for future research.