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Comparative analysis of cyclic sequences: Viroids and other small circular RNAs
German Conference on Bioinformatics
The analysis of small circular sequences requires specialized tools. While the differences between linear and circular sequences can be neglected in the case of long molecules such as bacterial genomes since in practice all analysis is performed in sequence windows, this is not true for viroids and related sequences which ...
Thermodynamics of RNA-RNA binding
German Conference on Bioinformatics 2005 (GCB 2005)
We present an extension of the standard partition function approach to RNA secondary structures that computes the probabilities Pu[i, j] that a sequence interval [i, j] is unpaired. Comparison with experimental data shows that Pu[i, j] can be applied as a significant determinant of local target site accessibility for RNA ...