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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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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Data provided by Europe PubMed Central.

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PMID: 17070713
RNAshapes: an integrated RNA analysis package based on abstract shapes.
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PMID: 16357029
CMfinder--a covariance model based RNA motif finding algorithm.
Yao Z, Weinberg Z, Ruzzo WL., Bioinformatics 22(4), 2006
PMID: 16357030
RNA thermometers.
Narberhaus F, Waldminghaus T, Chowdhury S., FEMS Microbiol Rev 30(1), 2006
PMID: 16438677
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PMID: 16500677
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Legendre M, Ritchie W, Lopez F, Gautheret D., PLoS Comput Biol 2(5), 2006
PMID: 16699595
Prediction of RNA secondary structure by free energy minimization.
Mathews DH, Turner DH., Curr Opin Struct Biol 16(3), 2006
PMID: 16713706
Dependence among sites in RNA evolution.
Yu J, Thorne JL., Mol Biol Evol 23(8), 2006
PMID: 16720696
Impact of RNA structure on the prediction of donor and acceptor splice sites.
Marashi SA, Eslahchi C, Pezeshk H, Sadeghi M., BMC Bioinformatics 7(), 2006
PMID: 16772025
Structural analysis of aligned RNAs.
Voss B., Nucleic Acids Res 34(19), 2006
PMID: 17020924
A benchmark of multiple sequence alignment programs upon structural RNAs.
Gardner PP, Wilm A, Washietl S., Nucleic Acids Res 33(8), 2005
PMID: 15860779
Computational screening of conserved genomic DNA in search of functional noncoding elements.
Bejerano G, Siepel AC, Kent WJ, Haussler D., Nat Methods 2(7), 2005
PMID: 16170870
P-RnaPredict--a parallel evolutionary algorithm for RNA folding: effects of pseudorandom number quality.
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PMID: 16220685

109 References

Data provided by Europe PubMed Central.

The European Large Subunit Ribosomal RNA Database.
Wuyts J, De Rijk P, Van de Peer Y, Winkelmans T, De Wachter R., Nucleic Acids Res. 29(1), 2001
PMID: 11125083
The European large subunit ribosomal RNA database
AUTHOR UNKNOWN, 0
The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs.
Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, Du Y, Feng B, Lin N, Madabusi LV, Muller KM, Pande N, Shang Z, Yu N, Gutell RR., BMC Bioinformatics 3(), 2002
PMID: 11869452
Gutell lab comparative RNA web site
AUTHOR UNKNOWN, 0
The European database on small subunit ribosomal RNA.
Wuyts J, Van de Peer Y, Winkelmans T, De Wachter R., Nucleic Acids Res. 30(1), 2002
PMID: 11752288
The European database on small subunit ribosomal RNA
AUTHOR UNKNOWN, 0
The Ribonuclease P Database.
Brown JW., Nucleic Acids Res. 27(1), 1999
PMID: 9847214
The ribonuclease P database
AUTHOR UNKNOWN, 0

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