Pairwise alignment method function, provides most of the functionality of rnaforester command line tool. Offers two different example for a local and global alignment.

Multiple alignment method function, provides most of the functionality of rnaforester command line tool. Offers one example.

Global, local and small-in-large alignment

Local similarity means finding the maximal similarity between substructures of RNA secondary structures. If these substructures are extended, the score decreases. This requires a scoring scheme that balances positive and negative scoring contributions. Otherwise, the similarity of the complete structures would always achieve the maximum score. It is generally assumed that an alignment of two empty structures scores zero. Local distance makes no sense, as empty forests have always the lowest possible distance of zero.

Substructures of RNA secondary structures in RNAforester are contiguous and ``closed'' by hairpin loops. The blue region shows a valid substructure. The green part of the structure is not closed because the closing hairpin is missing. The red part is a substructure that is not considered as a local structure for the same reason. This is less obvious, since only theU, which is a child of the root of this subtree, is not included. If the top-levelP node would not be included in the red substructure, this part would correspond to a closed subforest. The yellow part does not correspond to a closed subforest since the subtrees are not consecutive siblings.

Scoring models

Structural edit operations of Jiang et al.'s general edit model for RNA structures.

The sequence edit operationsbase match,base mismatch andbase deletion are the same for pairwise and multiple alignment. Abase pair breaking means the deletion of a base-pair bond. Abase-pair deletion is the composition of abase-pair breaking and twobase deletions. Abase-pair altering is treated likewise but there is only onebase-deletion involved. The structural edit operationsbase pair replacement and have a different effect for pairwise and multiple alignment. In pairwise alignment mode, the pairing bases are treated as a unit. In multiple alignment mode,base pair replacement score means the score for matching any base-pair plus the score for matching or mismatching the bases that pair. Thus, it is not possible to construct a base-pair dependend scoring for this model. The RIBOSUM scoring scheme are empirically derived base-pair and single base substitution scores that are available in pairwise alignment mode.