A comprehensive comparison of comparative RNA structure prediction approaches

Gardner PP, Giegerich R (2004)
BMC Bioinformatics 5(1): 140.

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Background: 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. Results: Here we evaluate a number of RNA folding algorithms using reliable RNA data-sets and compare their relative performance. Conclusions: 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.
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BMC Bioinformatics
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140
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Gardner PP, Giegerich R. A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics. 2004;5(1):140.
Gardner, P. P., & Giegerich, R. (2004). A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics, 5(1), 140. doi:10.1186/1471-2105-5-140
Gardner, P. P., and Giegerich, R. (2004). A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics 5, 140.
Gardner, P.P., & Giegerich, R., 2004. A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics, 5(1), p 140.
P.P. Gardner and R. Giegerich, “A comprehensive comparison of comparative RNA structure prediction approaches”, BMC Bioinformatics, vol. 5, 2004, pp. 140.
Gardner, P.P., Giegerich, R.: A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics. 5, 140 (2004).
Gardner, Paul P., and Giegerich, Robert. “A comprehensive comparison of comparative RNA structure prediction approaches”. BMC Bioinformatics 5.1 (2004): 140.
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AUTHOR UNKNOWN, 0
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ILM
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Algorithms for loop matchings
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CARNAC: folding families of related RNAs.
Touzet H, Perriquet O., Nucleic Acids Res. 32(Web Server issue), 2004
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Identification of consensus patterns in unaligned DNA sequences known to be functionally related.
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Dynalign
AUTHOR UNKNOWN, 0
Fast evaluation of internal loops in RNA secondary structure prediction.
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caRNAc
AUTHOR UNKNOWN, 0
RNAforester
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MARNA
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Infernal
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Rfam
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The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs.
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The ribonuclease P database
AUTHOR UNKNOWN, 0

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