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Gardner, Paul P.; Giegerich, Robert: A comprehensive comparison of comparative RNA structure prediction approaches. In: BMC Bioinformatics. Jg.5 H. 1. 2004
Inhalt
Structural alignments and consensus structures
Interpreting database information
Caveats
Use of defaults
Tool abuse
Standard of truth
Tools improve
Methods
Performance Measures
Results
Single sequence methods
Mfold & RNAfold
Sfold
Intrinsic limits of single sequence methods
Comparative method: alignment folding (plan A)
RNAalifold
Pfold
ILM
Comparative method: simultaneous sequence alignment and folding (plan B)
Sankoff
Foldalign
Dynalign
Carnac
Alignment of predicted structures (plan C)
RNA forester
MARNA
Discussion
Practical recommendations
Table 2
Table 3
Table 4
Table 5
Table 6
Table 7
Table 8
Table 9
Conclusions
Note added in proof
Authors' contributions
Acknowledgements
References