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Forest alignment with affine gaps and anchors, applied in RNA structure comparison. (English) Zbl 1292.68184
Summary: We present two enhancements to Jiang’s tree alignment algorithm, motivated by experience with its use for RNA structure alignment. One enhancement is the introduction of an affine gap model, which can be accommodated with a runtime increase by a constant factor. The second enhancement is a speed-up of the alignment algorithm when certain nodes in the trees are pre-aligned by a so-called anchoring. Both enhancements are included in a new implementation of the tool RNAforester. We evaluate the new algorithm with two applications related to RNA secondary structure analysis. Based on our experience, we suggest a new formulation of the tree alignment model, based on regular tree languages and rewrite rules.

MSC:
68W32 Algorithms on strings
68Q42 Grammars and rewriting systems
68Q45 Formal languages and automata
68R10 Graph theory (including graph drawing) in computer science
92D20 Protein sequences, DNA sequences
Software:
MUMMER; RNAforester
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